From 0e147950263b2e6494ea4c1fa0fa264511bb9bcd Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Tue, 10 Dec 2024 20:54:12 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@bf6c63719705a65ba98878638e383df789f60c1b=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- CODE_OF_CONDUCT.html | 2 +- CONTRIBUTING.html | 2 +- SUPPORT.html | 2 +- articles/TenX_data_download.html | 59 ++++++++-------- articles/guide_to_spatial_registration.html | 69 +++++++++---------- articles/index.html | 2 +- articles/multi_gene_plots.html | 45 ++++++------ articles/spatialLIBD.html | 49 +++++++------ authors.html | 2 +- index.html | 4 +- news/index.html | 2 +- pkgdown.yml | 2 +- reference/add10xVisiumAnalysis.html | 2 +- reference/add_images.html | 28 ++++---- reference/add_key.html | 4 +- reference/add_qc_metrics.html | 4 +- reference/annotate_registered_clusters.html | 4 +- reference/check_modeling_results.html | 4 +- reference/check_sce.html | 4 +- reference/check_sce_layer.html | 4 +- reference/check_spe.html | 4 +- reference/cluster_export.html | 4 +- reference/cluster_import.html | 8 +-- reference/enough_ram.html | 2 +- reference/fetch_data.html | 4 +- reference/frame_limits.html | 4 +- reference/gene_set_enrichment.html | 4 +- reference/gene_set_enrichment_plot.html | 4 +- reference/geom_spatial.html | 4 +- reference/get_colors.html | 4 +- reference/img_edit.html | 4 +- reference/img_update.html | 4 +- reference/img_update_all.html | 4 +- reference/index.html | 2 +- reference/layer_boxplot.html | 6 +- reference/layer_matrix_plot.html | 2 +- reference/layer_stat_cor.html | 4 +- reference/layer_stat_cor_plot.html | 4 +- reference/libd_layer_colors.html | 2 +- reference/locate_images.html | 2 +- reference/multi_gene_pca.html | 2 +- reference/multi_gene_sparsity.html | 2 +- reference/multi_gene_z_score.html | 2 +- reference/prep_stitched_data.html | 2 +- reference/read10xVisiumAnalysis.html | 2 +- reference/read10xVisiumWrapper.html | 2 +- reference/registration_block_cor.html | 14 ++-- reference/registration_model.html | 10 +-- reference/registration_pseudobulk.html | 8 +-- reference/registration_stats_anova.html | 20 +++--- reference/registration_stats_enrichment.html | 22 +++--- reference/registration_stats_pairwise.html | 22 +++--- reference/registration_wrapper.html | 26 +++---- reference/run_app.html | 2 +- reference/sce_to_spe.html | 4 +- reference/sig_genes_extract.html | 6 +- reference/sig_genes_extract_all.html | 6 +- reference/sort_clusters.html | 2 +- reference/spatialLIBD-package.html | 2 +- ..._Human_DLPFC_snRNAseq_Nguyen_topLayer.html | 2 +- reference/vis_clus.html | 4 +- reference/vis_clus_p.html | 4 +- reference/vis_gene.html | 4 +- reference/vis_gene_p.html | 4 +- reference/vis_grid_clus.html | 4 +- reference/vis_grid_gene.html | 4 +- 67 files changed, 275 insertions(+), 279 deletions(-) diff --git a/404.html b/404.html index 39748848..2e5b3fad 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 8de75ded..4beff552 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 9464221a..43356540 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/SUPPORT.html b/SUPPORT.html index 1b5752bc..9f4073d2 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index d6f3309e..6918603d 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -39,7 +39,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -117,7 +117,7 @@

Leonardo University
-

31 October 2024

+

10 December 2024

Source: vignettes/TenX_data_download.Rmd @@ -532,7 +532,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/4a1665ee0bf_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/ff86b3ad12c_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -818,11 +818,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-10-31 20:33:17.636373 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-10-31 20:33:29.208114 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-10-31 20:33:29.312782 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-10-31 20:33:29.55953 rtracklayer::import: reading the reference GTF file -#> 2024-10-31 20:33:57.419312 adding gene information to the SPE object +#> 2024-12-10 20:53:16.074157 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-12-10 20:53:27.483907 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-12-10 20:53:27.588653 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-12-10 20:53:27.833136 rtracklayer::import: reading the reference GTF file +#> 2024-12-10 20:53:55.523862 adding gene information to the SPE object #> Warning: Gene IDs did not match. This typically happens when you are not using #> the same GTF file as the one that was used by SpaceRanger. For example, one #> file uses GENCODE IDs and the other one ENSEMBL IDs. read10xVisiumWrapper() @@ -830,7 +830,7 @@

Wrapper functions#> Warning: Dropping 29 out of 36601 genes for which we don't have information on #> the reference GTF file. This typically happens when you are not using the same #> GTF file as the one that was used by SpaceRanger. -#> 2024-10-31 20:33:57.674576 adding information used by spatialLIBD +#> 2024-12-10 20:53:55.786291 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1114,9 +1114,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-10-31 20:33:58 UTC"
+
#> [1] "2024-12-10 20:53:56 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.682 mins
+
#> Time difference of 1.676 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1128,7 +1128,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-10-31
+#>  date     2024-12-10
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -1154,7 +1154,7 @@ 
Reproducibility#>  BiocStyle            * 2.32.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.1)
 #>  BiocVersion            3.19.1    2024-04-17 [2] Bioconductor 3.19 (R 4.4.1)
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@@ -1167,8 +1167,8 @@ 
Reproducibility#>  config                 0.3.2     2023-08-30 [1] RSPM (R 4.4.0)
 #>  cowplot                1.1.3     2024-01-22 [1] RSPM (R 4.4.0)
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-#>  data.table             1.16.2    2024-10-10 [1] RSPM (R 4.4.0)
+#>  curl                   6.0.1     2024-11-14 [2] RSPM (R 4.4.0)
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@@ -1204,7 +1204,6 @@ 
Reproducibility#>  gridExtra              2.3       2017-09-09 [1] RSPM (R 4.4.0)
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@@ -1215,19 +1214,19 @@ 
Reproducibility#>  jquerylib              0.1.4     2021-04-26 [2] RSPM (R 4.4.0)
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-#>  later                  1.3.2     2023-12-06 [2] RSPM (R 4.4.0)
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-#>  lubridate              1.9.3     2023-09-27 [1] RSPM (R 4.4.0)
+#>  lubridate              1.9.4     2024-12-08 [1] RSPM (R 4.4.0)
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-#>  maps                   3.4.2     2023-12-15 [1] RSPM (R 4.4.0)
+#>  maps                   3.4.2.1   2024-11-10 [1] RSPM (R 4.4.0)
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@@ -1242,16 +1241,16 @@ 
Reproducibility#>  plyr                   1.8.9     2023-10-02 [1] RSPM (R 4.4.0)
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-#>  promises               1.3.0     2024-04-05 [2] RSPM (R 4.4.0)
+#>  promises               1.3.2     2024-11-28 [2] RSPM (R 4.4.0)
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-#>  R.oo                   1.26.0    2024-01-24 [1] RSPM (R 4.4.0)
+#>  R.oo                   1.27.0    2024-11-01 [1] RSPM (R 4.4.0)
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-#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
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@@ -1261,9 +1260,9 @@ 
Reproducibility#>  Rhdf5lib               1.26.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
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-#>  rmarkdown              2.28      2024-08-17 [2] RSPM (R 4.4.0)
+#>  rmarkdown              2.29      2024-11-04 [2] RSPM (R 4.4.0)
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@@ -1281,13 +1280,13 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
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@@ -1325,7 +1324,7 @@ 
Bibliography[1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.28. 2024. URL:
+for R. R package version 2.29. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 

 

@@ -1413,7 +1412,7 @@ 
Bibliography[13]
 Y. Xie. knitr: A General-Purpose Package for Dynamic Report
-Generation in R. R package version 1.48. 2024. URL:
+Generation in R. R package version 1.49. 2024. URL:
 https://yihui.org/knitr/.
 

 
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index ad1cd9af..1fb42a39 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -101,7 +101,7 @@ 
Louise
 Development

       
                   
-            
31 October 2024

+            
10 December 2024

       
       Source: vignettes/guide_to_spatial_registration.Rmd
       
@@ -288,7 +288,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-10-31 20:30:20.090674 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-10 20:50:18.908873 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
 #>    t_stat_WM t_stat_Layer1 t_stat_Layer2 t_stat_Layer3 t_stat_Layer4
@@ -391,18 +391,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-10-31 20:30:27.935639 make pseudobulk object
-#> 2024-10-31 20:30:29.626031 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-10-31 20:30:29.686539 drop lowly expressed genes
-#> 2024-10-31 20:30:29.850742 normalize expression
-#> 2024-10-31 20:30:31.367735 create model matrix
-#> 2024-10-31 20:30:31.397973 run duplicateCorrelation()
-#> 2024-10-31 20:30:44.62648 The estimated correlation is: 0.138734774807097
-#> 2024-10-31 20:30:44.629237 computing enrichment statistics
-#> 2024-10-31 20:30:45.832523 extract and reformat enrichment results
-#> 2024-10-31 20:30:45.887797 running the baseline pairwise model
-#> 2024-10-31 20:30:46.027914 computing pairwise statistics
-#> 2024-10-31 20:30:47.409161 computing F-statistics

+#> 2024-12-10 20:50:26.693876 make pseudobulk object
+#> 2024-12-10 20:50:28.373776 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-12-10 20:50:28.433649 drop lowly expressed genes
+#> 2024-12-10 20:50:28.600077 normalize expression
+#> 2024-12-10 20:50:30.071241 create model matrix
+#> 2024-12-10 20:50:30.094844 run duplicateCorrelation()
+#> 2024-12-10 20:50:43.158967 The estimated correlation is: 0.138734774807097
+#> 2024-12-10 20:50:43.161715 computing enrichment statistics
+#> 2024-12-10 20:50:44.291205 extract and reformat enrichment results
+#> 2024-12-10 20:50:44.346711 running the baseline pairwise model
+#> 2024-12-10 20:50:44.486952 computing pairwise statistics
+#> 2024-12-10 20:50:45.835991 computing F-statistics

Extract Enrichment t-statistics @@ -562,9 +562,9 @@

Reproducibilitylibrary("knitr") knit("guide_to_spatial_registration.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-10-31 20:30:48 UTC"
+
#> [1] "2024-12-10 20:50:47 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 41.483 secs
+
#> Time difference of 41.04 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -576,7 +576,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
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-#>  date     2024-10-31
+#>  date     2024-12-10
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 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -602,7 +602,7 @@ 
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-#>  curl                   5.2.3     2024-09-20 [2] RSPM (R 4.4.0)
-#>  data.table             1.16.2    2024-10-10 [1] RSPM (R 4.4.0)
+#>  curl                   6.0.1     2024-11-14 [2] RSPM (R 4.4.0)
+#>  data.table             1.16.4    2024-12-06 [1] RSPM (R 4.4.0)
 #>  DBI                    1.2.3     2024-06-02 [1] RSPM (R 4.4.0)
 #>  dbplyr                 2.5.0     2024-03-19 [1] RSPM (R 4.4.0)
 #>  DelayedArray           0.30.1    2024-05-07 [1] Bioconductor 3.19 (R 4.4.1)
@@ -648,7 +648,6 @@ 
Reproducibility#>  golem                  0.5.1     2024-08-27 [1] RSPM (R 4.4.0)
 #>  gridExtra              2.3       2017-09-09 [1] RSPM (R 4.4.0)
 #>  gtable                 0.3.6     2024-10-25 [1] RSPM (R 4.4.0)
-#>  highr                  0.11      2024-05-26 [2] RSPM (R 4.4.0)
 #>  htmltools              0.5.8.1   2024-04-04 [2] RSPM (R 4.4.0)
 #>  htmlwidgets            1.6.4     2023-12-06 [2] RSPM (R 4.4.0)
 #>  httpuv                 1.6.15    2024-03-26 [2] RSPM (R 4.4.0)
@@ -659,17 +658,17 @@ 
Reproducibility#>  jquerylib              0.1.4     2021-04-26 [2] RSPM (R 4.4.0)
 #>  jsonlite               1.8.9     2024-09-20 [2] RSPM (R 4.4.0)
 #>  KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.1)
-#>  knitr                  1.48      2024-07-07 [2] RSPM (R 4.4.0)
-#>  later                  1.3.2     2023-12-06 [2] RSPM (R 4.4.0)
+#>  knitr                  1.49      2024-11-08 [2] RSPM (R 4.4.0)
+#>  later                  1.4.1     2024-11-27 [2] RSPM (R 4.4.0)
 #>  lattice                0.22-6    2024-03-20 [3] CRAN (R 4.4.1)
 #>  lazyeval               0.2.2     2019-03-15 [1] RSPM (R 4.4.0)
 #>  lifecycle              1.0.4     2023-11-07 [2] RSPM (R 4.4.0)
 #>  limma                  3.60.6    2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
 #>  locfit                 1.5-9.10  2024-06-24 [1] RSPM (R 4.4.0)
-#>  lubridate              1.9.3     2023-09-27 [1] RSPM (R 4.4.0)
+#>  lubridate              1.9.4     2024-12-08 [1] RSPM (R 4.4.0)
 #>  magick                 2.8.5     2024-09-20 [1] RSPM (R 4.4.0)
 #>  magrittr               2.0.3     2022-03-30 [2] RSPM (R 4.4.0)
-#>  maps                   3.4.2     2023-12-15 [1] RSPM (R 4.4.0)
+#>  maps                   3.4.2.1   2024-11-10 [1] RSPM (R 4.4.0)
 #>  Matrix                 1.7-1     2024-10-18 [3] RSPM (R 4.4.0)
 #>  MatrixGenerics       * 1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  matrixStats          * 1.4.1     2024-09-08 [1] RSPM (R 4.4.0)
@@ -683,22 +682,22 @@ 
Reproducibility#>  plotly                 4.10.4    2024-01-13 [1] RSPM (R 4.4.0)
 #>  plyr                   1.8.9     2023-10-02 [1] RSPM (R 4.4.0)
 #>  png                    0.1-8     2022-11-29 [1] RSPM (R 4.4.0)
-#>  promises               1.3.0     2024-04-05 [2] RSPM (R 4.4.0)
+#>  promises               1.3.2     2024-11-28 [2] RSPM (R 4.4.0)
 #>  purrr                  1.0.2     2023-08-10 [2] RSPM (R 4.4.0)
 #>  R6                     2.5.1     2021-08-19 [2] RSPM (R 4.4.0)
 #>  ragg                   1.3.3     2024-09-11 [2] RSPM (R 4.4.0)
 #>  rappdirs               0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
 #>  RColorBrewer           1.1-3     2022-04-03 [1] RSPM (R 4.4.0)
-#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
+#>  Rcpp                   1.0.13-1  2024-11-02 [2] RSPM (R 4.4.0)
 #>  RCurl                  1.98-1.16 2024-07-11 [1] RSPM (R 4.4.0)
 #>  RefManageR           * 1.4.0     2022-09-30 [1] RSPM (R 4.4.0)
 #>  rematch2               2.1.2     2020-05-01 [2] RSPM (R 4.4.0)
 #>  restfulr               0.0.15    2022-06-16 [1] RSPM (R 4.4.1)
 #>  rjson                  0.2.23    2024-09-16 [1] RSPM (R 4.4.0)
 #>  rlang                  1.1.4     2024-06-04 [2] RSPM (R 4.4.0)
-#>  rmarkdown              2.28      2024-08-17 [2] RSPM (R 4.4.0)
+#>  rmarkdown              2.29      2024-11-04 [2] RSPM (R 4.4.0)
 #>  Rsamtools              2.20.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
-#>  RSQLite                2.3.7     2024-05-27 [1] RSPM (R 4.4.0)
+#>  RSQLite                2.3.9     2024-12-03 [1] RSPM (R 4.4.0)
 #>  rsvd                   1.0.5     2021-04-16 [1] RSPM (R 4.4.0)
 #>  rtracklayer            1.64.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  S4Arrays               1.4.1     2024-05-20 [1] Bioconductor 3.19 (R 4.4.1)
@@ -716,13 +715,13 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.10   2024-10-31 [1] Bioconductor
+#>  spatialLIBD          * 1.19.0    2024-12-10 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
 #>  SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
 #>  systemfonts            1.1.0     2024-05-15 [2] RSPM (R 4.4.0)
-#>  textshaping            0.4.0     2024-05-24 [2] RSPM (R 4.4.0)
+#>  textshaping            0.4.1     2024-12-06 [2] RSPM (R 4.4.0)
 #>  tibble                 3.2.1     2023-03-20 [2] RSPM (R 4.4.0)
 #>  tidyr                  1.3.1     2024-01-24 [1] RSPM (R 4.4.0)
 #>  tidyselect             1.2.1     2024-03-11 [1] RSPM (R 4.4.0)
@@ -734,7 +733,7 @@ 
Reproducibility#>  viridis                0.6.5     2024-01-29 [1] RSPM (R 4.4.0)
 #>  viridisLite            0.4.2     2023-05-02 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.2     2024-10-28 [2] RSPM (R 4.4.0)
-#>  xfun                   0.48      2024-10-03 [2] RSPM (R 4.4.0)
+#>  xfun                   0.49      2024-10-31 [2] RSPM (R 4.4.0)
 #>  XML                    3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
 #>  xml2                   1.3.6     2023-12-04 [2] RSPM (R 4.4.0)
 #>  xtable                 1.8-4     2019-04-21 [2] RSPM (R 4.4.0)
@@ -760,7 +759,7 @@ 
Bibliography[1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.28. 2024. URL:
+for R. R package version 2.29. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 

 

@@ -825,7 +824,7 @@ 
Bibliography[10]
 Y. Xie. knitr: A General-Purpose Package for Dynamic Report
-Generation in R. R package version 1.48. 2024. URL:
+Generation in R. R package version 1.49. 2024. URL:
 https://yihui.org/knitr/.
 

 
diff --git a/articles/index.html b/articles/index.html
index 4eb170f7..b735f2ff 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 5a54b5fc..97a98ee6 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -108,7 +108,7 @@ 
Leonardo
 Public Health

       
                   
-            
31 October 2024

+            
10 December 2024

       
       Source: vignettes/multi_gene_plots.Rmd
       
@@ -195,9 +195,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-10-31 20:31:14.755233 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-10 20:51:13.202364 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-10-31 20:31:15.950342 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:51:14.409801 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -421,9 +421,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-10-31 20:31:32 UTC"

+
#> [1] "2024-12-10 20:51:30 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 37.985 secs

+
#> Time difference of 37.939 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -435,7 +435,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-10-31
+#>  date     2024-12-10
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -461,7 +461,7 @@ 
Reproducibility#>  BiocStyle            * 2.32.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.1)
 #>  BiocVersion            3.19.1    2024-04-17 [2] Bioconductor 3.19 (R 4.4.1)
 #>  Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.1)
-#>  bit                    4.5.0     2024-09-20 [1] RSPM (R 4.4.0)
+#>  bit                    4.5.0.1   2024-12-03 [1] RSPM (R 4.4.0)
 #>  bit64                  4.5.2     2024-09-22 [1] RSPM (R 4.4.0)
 #>  bitops                 1.0-9     2024-10-03 [1] RSPM (R 4.4.0)
 #>  blob                   1.2.4     2023-03-17 [1] RSPM (R 4.4.0)
@@ -474,8 +474,8 @@ 
Reproducibility#>  config                 0.3.2     2023-08-30 [1] RSPM (R 4.4.0)
 #>  cowplot                1.1.3     2024-01-22 [1] RSPM (R 4.4.0)
 #>  crayon                 1.5.3     2024-06-20 [2] RSPM (R 4.4.0)
-#>  curl                   5.2.3     2024-09-20 [2] RSPM (R 4.4.0)
-#>  data.table             1.16.2    2024-10-10 [1] RSPM (R 4.4.0)
+#>  curl                   6.0.1     2024-11-14 [2] RSPM (R 4.4.0)
+#>  data.table             1.16.4    2024-12-06 [1] RSPM (R 4.4.0)
 #>  DBI                    1.2.3     2024-06-02 [1] RSPM (R 4.4.0)
 #>  dbplyr                 2.5.0     2024-03-19 [1] RSPM (R 4.4.0)
 #>  DelayedArray           0.30.1    2024-05-07 [1] Bioconductor 3.19 (R 4.4.1)
@@ -508,7 +508,6 @@ 
Reproducibility#>  golem                  0.5.1     2024-08-27 [1] RSPM (R 4.4.0)
 #>  gridExtra              2.3       2017-09-09 [1] RSPM (R 4.4.0)
 #>  gtable                 0.3.6     2024-10-25 [1] RSPM (R 4.4.0)
-#>  highr                  0.11      2024-05-26 [2] RSPM (R 4.4.0)
 #>  htmltools              0.5.8.1   2024-04-04 [2] RSPM (R 4.4.0)
 #>  htmlwidgets            1.6.4     2023-12-06 [2] RSPM (R 4.4.0)
 #>  httpuv                 1.6.15    2024-03-26 [2] RSPM (R 4.4.0)
@@ -519,18 +518,18 @@ 
Reproducibility#>  jquerylib              0.1.4     2021-04-26 [2] RSPM (R 4.4.0)
 #>  jsonlite               1.8.9     2024-09-20 [2] RSPM (R 4.4.0)
 #>  KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.1)
-#>  knitr                  1.48      2024-07-07 [2] RSPM (R 4.4.0)
+#>  knitr                  1.49      2024-11-08 [2] RSPM (R 4.4.0)
 #>  labeling               0.4.3     2023-08-29 [1] RSPM (R 4.4.0)
-#>  later                  1.3.2     2023-12-06 [2] RSPM (R 4.4.0)
+#>  later                  1.4.1     2024-11-27 [2] RSPM (R 4.4.0)
 #>  lattice                0.22-6    2024-03-20 [3] CRAN (R 4.4.1)
 #>  lazyeval               0.2.2     2019-03-15 [1] RSPM (R 4.4.0)
 #>  lifecycle              1.0.4     2023-11-07 [2] RSPM (R 4.4.0)
 #>  limma                  3.60.6    2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
 #>  locfit                 1.5-9.10  2024-06-24 [1] RSPM (R 4.4.0)
-#>  lubridate              1.9.3     2023-09-27 [1] RSPM (R 4.4.0)
+#>  lubridate              1.9.4     2024-12-08 [1] RSPM (R 4.4.0)
 #>  magick                 2.8.5     2024-09-20 [1] RSPM (R 4.4.0)
 #>  magrittr               2.0.3     2022-03-30 [2] RSPM (R 4.4.0)
-#>  maps                   3.4.2     2023-12-15 [1] RSPM (R 4.4.0)
+#>  maps                   3.4.2.1   2024-11-10 [1] RSPM (R 4.4.0)
 #>  Matrix                 1.7-1     2024-10-18 [3] RSPM (R 4.4.0)
 #>  MatrixGenerics       * 1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  matrixStats          * 1.4.1     2024-09-08 [1] RSPM (R 4.4.0)
@@ -544,22 +543,22 @@ 
Reproducibility#>  plotly                 4.10.4    2024-01-13 [1] RSPM (R 4.4.0)
 #>  plyr                   1.8.9     2023-10-02 [1] RSPM (R 4.4.0)
 #>  png                    0.1-8     2022-11-29 [1] RSPM (R 4.4.0)
-#>  promises               1.3.0     2024-04-05 [2] RSPM (R 4.4.0)
+#>  promises               1.3.2     2024-11-28 [2] RSPM (R 4.4.0)
 #>  purrr                  1.0.2     2023-08-10 [2] RSPM (R 4.4.0)
 #>  R6                     2.5.1     2021-08-19 [2] RSPM (R 4.4.0)
 #>  ragg                   1.3.3     2024-09-11 [2] RSPM (R 4.4.0)
 #>  rappdirs               0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
 #>  RColorBrewer           1.1-3     2022-04-03 [1] RSPM (R 4.4.0)
-#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
+#>  Rcpp                   1.0.13-1  2024-11-02 [2] RSPM (R 4.4.0)
 #>  RCurl                  1.98-1.16 2024-07-11 [1] RSPM (R 4.4.0)
 #>  RefManageR           * 1.4.0     2022-09-30 [1] RSPM (R 4.4.0)
 #>  rematch2               2.1.2     2020-05-01 [2] RSPM (R 4.4.0)
 #>  restfulr               0.0.15    2022-06-16 [1] RSPM (R 4.4.1)
 #>  rjson                  0.2.23    2024-09-16 [1] RSPM (R 4.4.0)
 #>  rlang                  1.1.4     2024-06-04 [2] RSPM (R 4.4.0)
-#>  rmarkdown              2.28      2024-08-17 [2] RSPM (R 4.4.0)
+#>  rmarkdown              2.29      2024-11-04 [2] RSPM (R 4.4.0)
 #>  Rsamtools              2.20.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
-#>  RSQLite                2.3.7     2024-05-27 [1] RSPM (R 4.4.0)
+#>  RSQLite                2.3.9     2024-12-03 [1] RSPM (R 4.4.0)
 #>  rsvd                   1.0.5     2021-04-16 [1] RSPM (R 4.4.0)
 #>  rtracklayer            1.64.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  S4Arrays               1.4.1     2024-05-20 [1] Bioconductor 3.19 (R 4.4.1)
@@ -577,13 +576,13 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.10   2024-10-31 [1] Bioconductor
+#>  spatialLIBD          * 1.19.0    2024-12-10 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
 #>  SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
 #>  systemfonts            1.1.0     2024-05-15 [2] RSPM (R 4.4.0)
-#>  textshaping            0.4.0     2024-05-24 [2] RSPM (R 4.4.0)
+#>  textshaping            0.4.1     2024-12-06 [2] RSPM (R 4.4.0)
 #>  tibble                 3.2.1     2023-03-20 [2] RSPM (R 4.4.0)
 #>  tidyr                  1.3.1     2024-01-24 [1] RSPM (R 4.4.0)
 #>  tidyselect             1.2.1     2024-03-11 [1] RSPM (R 4.4.0)
@@ -595,7 +594,7 @@ 
Reproducibility#>  viridis                0.6.5     2024-01-29 [1] RSPM (R 4.4.0)
 #>  viridisLite            0.4.2     2023-05-02 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.2     2024-10-28 [2] RSPM (R 4.4.0)
-#>  xfun                   0.48      2024-10-03 [2] RSPM (R 4.4.0)
+#>  xfun                   0.49      2024-10-31 [2] RSPM (R 4.4.0)
 #>  XML                    3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
 #>  xml2                   1.3.6     2023-12-04 [2] RSPM (R 4.4.0)
 #>  xtable                 1.8-4     2019-04-21 [2] RSPM (R 4.4.0)
@@ -622,7 +621,7 @@ 
Bibliography[1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.28. 2024. URL:
+for R. R package version 2.29. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 

 

diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index dbb8f739..8e3e0471 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -39,7 +39,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -114,7 +114,7 @@ 
Andrew E.
 Campus

       
                   
-            
31 October 2024

+            
10 December 2024

       
       Source: vignettes/spatialLIBD.Rmd
       
@@ -414,7 +414,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-10-31 20:31:48.544302 loading file /github/home/.cache/R/BiocFileCache/4a115950912_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-10 20:51:46.846798 loading file /github/home/.cache/R/BiocFileCache/ff843b7fdca_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -426,9 +426,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-10-31 20:31:55.311001 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:51:53.741477 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-10-31 20:31:55.78616 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-12-10 20:51:54.19866 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

 
Once you have downloaded the objects, we can explore them a little
 bit

 
@@ -501,7 +501,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.250   0.380   9.653
+#>   9.306   0.396   9.727
 
 ## Explore the result
 class(sig_genes)
@@ -1377,9 +1377,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-10-31 20:32:13 UTC"

+
#> [1] "2024-12-10 20:52:12 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 37.911 secs

+
#> Time difference of 38.252 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1391,7 +1391,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-10-31
+#>  date     2024-12-10
 #>  pandoc   3.2 @ /usr/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -1417,7 +1417,7 @@ 
Reproducibility#>  BiocStyle            * 2.32.1    2024-06-16 [1] Bioconductor 3.19 (R 4.4.1)
 #>  BiocVersion            3.19.1    2024-04-17 [2] Bioconductor 3.19 (R 4.4.1)
 #>  Biostrings             2.72.1    2024-06-02 [1] Bioconductor 3.19 (R 4.4.1)
-#>  bit                    4.5.0     2024-09-20 [1] RSPM (R 4.4.0)
+#>  bit                    4.5.0.1   2024-12-03 [1] RSPM (R 4.4.0)
 #>  bit64                  4.5.2     2024-09-22 [1] RSPM (R 4.4.0)
 #>  bitops                 1.0-9     2024-10-03 [1] RSPM (R 4.4.0)
 #>  blob                   1.2.4     2023-03-17 [1] RSPM (R 4.4.0)
@@ -1430,8 +1430,8 @@ 
Reproducibility#>  config                 0.3.2     2023-08-30 [1] RSPM (R 4.4.0)
 #>  cowplot                1.1.3     2024-01-22 [1] RSPM (R 4.4.0)
 #>  crayon                 1.5.3     2024-06-20 [2] RSPM (R 4.4.0)
-#>  curl                   5.2.3     2024-09-20 [2] RSPM (R 4.4.0)
-#>  data.table             1.16.2    2024-10-10 [1] RSPM (R 4.4.0)
+#>  curl                   6.0.1     2024-11-14 [2] RSPM (R 4.4.0)
+#>  data.table             1.16.4    2024-12-06 [1] RSPM (R 4.4.0)
 #>  DBI                    1.2.3     2024-06-02 [1] RSPM (R 4.4.0)
 #>  dbplyr                 2.5.0     2024-03-19 [1] RSPM (R 4.4.0)
 #>  DelayedArray           0.30.1    2024-05-07 [1] Bioconductor 3.19 (R 4.4.1)
@@ -1464,7 +1464,6 @@ 
Reproducibility#>  golem                  0.5.1     2024-08-27 [1] RSPM (R 4.4.0)
 #>  gridExtra              2.3       2017-09-09 [1] RSPM (R 4.4.0)
 #>  gtable                 0.3.6     2024-10-25 [1] RSPM (R 4.4.0)
-#>  highr                  0.11      2024-05-26 [2] RSPM (R 4.4.0)
 #>  htmltools              0.5.8.1   2024-04-04 [2] RSPM (R 4.4.0)
 #>  htmlwidgets            1.6.4     2023-12-06 [2] RSPM (R 4.4.0)
 #>  httpuv                 1.6.15    2024-03-26 [2] RSPM (R 4.4.0)
@@ -1475,18 +1474,18 @@ 
Reproducibility#>  jquerylib              0.1.4     2021-04-26 [2] RSPM (R 4.4.0)
 #>  jsonlite               1.8.9     2024-09-20 [2] RSPM (R 4.4.0)
 #>  KEGGREST               1.44.1    2024-06-19 [1] Bioconductor 3.19 (R 4.4.1)
-#>  knitr                  1.48      2024-07-07 [2] RSPM (R 4.4.0)
+#>  knitr                  1.49      2024-11-08 [2] RSPM (R 4.4.0)
 #>  labeling               0.4.3     2023-08-29 [1] RSPM (R 4.4.0)
-#>  later                  1.3.2     2023-12-06 [2] RSPM (R 4.4.0)
+#>  later                  1.4.1     2024-11-27 [2] RSPM (R 4.4.0)
 #>  lattice                0.22-6    2024-03-20 [3] CRAN (R 4.4.1)
 #>  lazyeval               0.2.2     2019-03-15 [1] RSPM (R 4.4.0)
 #>  lifecycle              1.0.4     2023-11-07 [2] RSPM (R 4.4.0)
 #>  limma                  3.60.6    2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
 #>  locfit                 1.5-9.10  2024-06-24 [1] RSPM (R 4.4.0)
-#>  lubridate              1.9.3     2023-09-27 [1] RSPM (R 4.4.0)
+#>  lubridate              1.9.4     2024-12-08 [1] RSPM (R 4.4.0)
 #>  magick                 2.8.5     2024-09-20 [1] RSPM (R 4.4.0)
 #>  magrittr               2.0.3     2022-03-30 [2] RSPM (R 4.4.0)
-#>  maps                   3.4.2     2023-12-15 [1] RSPM (R 4.4.0)
+#>  maps                   3.4.2.1   2024-11-10 [1] RSPM (R 4.4.0)
 #>  Matrix                 1.7-1     2024-10-18 [3] RSPM (R 4.4.0)
 #>  MatrixGenerics       * 1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  matrixStats          * 1.4.1     2024-09-08 [1] RSPM (R 4.4.0)
@@ -1500,22 +1499,22 @@ 
Reproducibility#>  plotly                 4.10.4    2024-01-13 [1] RSPM (R 4.4.0)
 #>  plyr                   1.8.9     2023-10-02 [1] RSPM (R 4.4.0)
 #>  png                    0.1-8     2022-11-29 [1] RSPM (R 4.4.0)
-#>  promises               1.3.0     2024-04-05 [2] RSPM (R 4.4.0)
+#>  promises               1.3.2     2024-11-28 [2] RSPM (R 4.4.0)
 #>  purrr                  1.0.2     2023-08-10 [2] RSPM (R 4.4.0)
 #>  R6                     2.5.1     2021-08-19 [2] RSPM (R 4.4.0)
 #>  ragg                   1.3.3     2024-09-11 [2] RSPM (R 4.4.0)
 #>  rappdirs               0.3.3     2021-01-31 [2] RSPM (R 4.4.0)
 #>  RColorBrewer           1.1-3     2022-04-03 [1] RSPM (R 4.4.0)
-#>  Rcpp                   1.0.13    2024-07-17 [2] RSPM (R 4.4.0)
+#>  Rcpp                   1.0.13-1  2024-11-02 [2] RSPM (R 4.4.0)
 #>  RCurl                  1.98-1.16 2024-07-11 [1] RSPM (R 4.4.0)
 #>  RefManageR           * 1.4.0     2022-09-30 [1] RSPM (R 4.4.0)
 #>  rematch2               2.1.2     2020-05-01 [2] RSPM (R 4.4.0)
 #>  restfulr               0.0.15    2022-06-16 [1] RSPM (R 4.4.1)
 #>  rjson                  0.2.23    2024-09-16 [1] RSPM (R 4.4.0)
 #>  rlang                  1.1.4     2024-06-04 [2] RSPM (R 4.4.0)
-#>  rmarkdown              2.28      2024-08-17 [2] RSPM (R 4.4.0)
+#>  rmarkdown              2.29      2024-11-04 [2] RSPM (R 4.4.0)
 #>  Rsamtools              2.20.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
-#>  RSQLite                2.3.7     2024-05-27 [1] RSPM (R 4.4.0)
+#>  RSQLite                2.3.9     2024-12-03 [1] RSPM (R 4.4.0)
 #>  rsvd                   1.0.5     2021-04-16 [1] RSPM (R 4.4.0)
 #>  rtracklayer            1.64.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  S4Arrays               1.4.1     2024-05-20 [1] Bioconductor 3.19 (R 4.4.1)
@@ -1533,13 +1532,13 @@ 
Reproducibility#>  SparseArray            1.4.8     2024-05-24 [1] Bioconductor 3.19 (R 4.4.1)
 #>  sparseMatrixStats      1.16.0    2024-04-30 [1] Bioconductor 3.19 (R 4.4.1)
 #>  SpatialExperiment    * 1.14.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
-#>  spatialLIBD          * 1.17.10   2024-10-31 [1] Bioconductor
+#>  spatialLIBD          * 1.19.0    2024-12-10 [1] Bioconductor
 #>  statmod                1.5.0     2023-01-06 [1] RSPM (R 4.4.0)
 #>  stringi                1.8.4     2024-05-06 [2] RSPM (R 4.4.0)
 #>  stringr                1.5.1     2023-11-14 [2] RSPM (R 4.4.0)
 #>  SummarizedExperiment * 1.34.0    2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
 #>  systemfonts            1.1.0     2024-05-15 [2] RSPM (R 4.4.0)
-#>  textshaping            0.4.0     2024-05-24 [2] RSPM (R 4.4.0)
+#>  textshaping            0.4.1     2024-12-06 [2] RSPM (R 4.4.0)
 #>  tibble                 3.2.1     2023-03-20 [2] RSPM (R 4.4.0)
 #>  tidyr                  1.3.1     2024-01-24 [1] RSPM (R 4.4.0)
 #>  tidyselect             1.2.1     2024-03-11 [1] RSPM (R 4.4.0)
@@ -1551,7 +1550,7 @@ 
Reproducibility#>  viridis                0.6.5     2024-01-29 [1] RSPM (R 4.4.0)
 #>  viridisLite            0.4.2     2023-05-02 [1] RSPM (R 4.4.0)
 #>  withr                  3.0.2     2024-10-28 [2] RSPM (R 4.4.0)
-#>  xfun                   0.48      2024-10-03 [2] RSPM (R 4.4.0)
+#>  xfun                   0.49      2024-10-31 [2] RSPM (R 4.4.0)
 #>  XML                    3.99-0.17 2024-06-25 [1] RSPM (R 4.4.0)
 #>  xml2                   1.3.6     2023-12-04 [2] RSPM (R 4.4.0)
 #>  xtable                 1.8-4     2019-04-21 [2] RSPM (R 4.4.0)
@@ -1577,7 +1576,7 @@ 
Bibliography[1]
 J. Allaire, Y. Xie, C. Dervieux, et al. rmarkdown: Dynamic Documents
-for R. R package version 2.28. 2024. URL:
+for R. R package version 2.29. 2024. URL:
 https://github.com/rstudio/rmarkdown.
 

 

diff --git a/authors.html b/authors.html
index 5937875b..476bcfc8 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
diff --git a/index.html b/index.html
index dbbc25ee..696f4d39 100644
--- a/index.html
+++ b/index.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -544,7 +544,7 @@ 
Dev status

 
  • Bioc last commit
    • 
 
  • Bioc dependencies
    • 
 
  • Codecov test coverage
    • 
-
  • R build status
    • 
+
  • R-CMD-check-bioc
    • 
 
  • GitHub issues
    • 
 
  • GitHub pulls
    • 
 
  • DOI
    • 
diff --git a/news/index.html b/news/index.html
index 1a8180aa..07752004 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
diff --git a/pkgdown.yml b/pkgdown.yml
index 5d936436..c1b06d40 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,4 +6,4 @@ articles:
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
   TenX_data_download: TenX_data_download.html
-last_built: 2024-10-31T20:24Z
+last_built: 2024-12-10T20:44Z
diff --git a/reference/add10xVisiumAnalysis.html b/reference/add10xVisiumAnalysis.html
index 72a96530..7be499c9 100644
--- a/reference/add10xVisiumAnalysis.html
+++ b/reference/add10xVisiumAnalysis.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
diff --git a/reference/add_images.html b/reference/add_images.html
index d759c6c7..7789f964 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -165,29 +165,29 @@ 
    Examples
    
         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-10-31 20:24:19.062387 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-10-31 20:24:34.560494 adding image for sample 151507
-#> 2024-10-31 20:24:36.193818 adding image for sample 151508
+#> 2024-12-10 20:44:19.980766 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:44:35.401937 adding image for sample 151507
+#> 2024-12-10 20:44:37.006964 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-10-31 20:24:36.194563 adding image for sample 151509
+#> 2024-12-10 20:44:37.00772 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-10-31 20:24:36.195075 adding image for sample 151510
+#> 2024-12-10 20:44:37.008243 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-10-31 20:24:36.195568 adding image for sample 151669
+#> 2024-12-10 20:44:37.008723 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-10-31 20:24:36.196038 adding image for sample 151670
+#> 2024-12-10 20:44:37.009222 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-10-31 20:24:36.196534 adding image for sample 151671
+#> 2024-12-10 20:44:37.009733 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-10-31 20:24:36.197004 adding image for sample 151672
+#> 2024-12-10 20:44:37.010203 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-10-31 20:24:36.197478 adding image for sample 151673
+#> 2024-12-10 20:44:37.010661 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-10-31 20:24:36.19794 adding image for sample 151674
+#> 2024-12-10 20:44:37.011127 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-10-31 20:24:36.198402 adding image for sample 151675
+#> 2024-12-10 20:44:37.011592 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-10-31 20:24:36.198871 adding image for sample 151676
+#> 2024-12-10 20:44:37.012058 adding image for sample 151676
 #> Warning: No image was found for sample: 151676
 #> DataFrame with 13 rows and 4 columns
 #>       sample_id    image_id   data scaleFactor
diff --git a/reference/add_key.html b/reference/add_key.html
index f431e89c..b8e7e8e5 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -124,7 +124,7 @@ 
    Examples
    
     spe$key_original <- NULL
     head(spe$key)
 }
-#> 2024-10-31 20:24:38.980763 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:44:39.822613 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "151507_AAACAACGAATAGTTC-1" "151507_AAACAAGTATCTCCCA-1"
 #> [3] "151507_AAACAATCTACTAGCA-1" "151507_AAACACCAATAACTGC-1"
 #> [5] "151507_AAACAGCTTTCAGAAG-1" "151507_AAACAGGGTCTATATT-1"
diff --git a/reference/add_qc_metrics.html b/reference/add_qc_metrics.html
index c16abd27..ecb4f1ab 100644
--- a/reference/add_qc_metrics.html
+++ b/reference/add_qc_metrics.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -144,7 +144,7 @@ 
    Author
    
     
    Examples
    
     
    ## Obtain the necessary data
 spe_pre_qc <- fetch_data("spatialDLPFC_Visium_example_subset")
-#> 2024-10-31 20:24:55.026698 loading file /github/home/.cache/R/BiocFileCache/4a160c71130_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
+#> 2024-12-10 20:44:55.787804 loading file /github/home/.cache/R/BiocFileCache/ff84b9ecfd8_spatialDLPFC_spe_subset_example.rds%3Fdl%3D1
 
 ## For now, we fake out tissue spots in example data
 spe_qc <- spe_pre_qc
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index ee2b27d6..3f280498 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
    
 
@@ -137,7 +137,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 20:25:07.681774 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-10 20:45:08.429686 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the correlations
 cor_stats_layer <- layer_stat_cor(
diff --git a/reference/check_modeling_results.html b/reference/check_modeling_results.html
index 2f490bed..bf544197 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -108,7 +108,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 20:25:09.047655 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-10 20:45:09.789792 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Check the object
 xx <- check_modeling_results(modeling_results)
diff --git a/reference/check_sce.html b/reference/check_sce.html
index 0178a36b..d59ec1f9 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -131,7 +131,7 @@ 
    Examples
    
     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-10-31 20:25:10.442552 loading file /github/home/.cache/R/BiocFileCache/4a115950912_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-12-10 20:45:11.204659 loading file /github/home/.cache/R/BiocFileCache/ff843b7fdca_sce_sub_for_vignette.Rdata%3Fdl%3D1
 #> class: SingleCellExperiment 
 #> dim: 33538 47681 
 #> metadata(1): image
diff --git a/reference/check_sce_layer.html b/reference/check_sce_layer.html
index 84c1ec54..db0075cb 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -112,7 +112,7 @@ 
    Examples
    
 ## Obtain example data from the HumanPilot project
 ## (Maynard, Collado-Torres, et al, 2021)
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-31 20:25:13.134764 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:45:14.016212 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the pseudo-bulked data
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index e345ef21..e63c291d 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -123,7 +123,7 @@ 
    Examples
    
     ## Check the object
     check_spe(spe)
 }
-#> 2024-10-31 20:25:14.606332 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:45:15.508607 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> class: SpatialExperiment 
 #> dim: 33538 47681 
 #> metadata(0):
diff --git a/reference/cluster_export.html b/reference/cluster_export.html
index a0cf464f..feb83609 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -21,7 +21,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -134,7 +134,7 @@ 
    Examples
    
     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-10-31 20:25:30.508778 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:45:30.613937 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 
    
diff --git a/reference/cluster_import.html b/reference/cluster_import.html
index 3e213df5..f9a6fd18 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -137,11 +137,11 @@ 
    Examples
    
     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-10-31 20:25:45.336307 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:45:46.320682 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpgTDK7X/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/RtmprQdFX7/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/RtmpgTDK7X/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/RtmprQdFX7/exported_clusters/GraphBased' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
 #> DataFrame with 47681 rows and 71 columns
 #>                                       key   sample_id   Cluster   sum_umi
diff --git a/reference/enough_ram.html b/reference/enough_ram.html
index 565d75f9..d16988a1 100644
--- a/reference/enough_ram.html
+++ b/reference/enough_ram.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
diff --git a/reference/fetch_data.html b/reference/fetch_data.html
index e50775cf..4e68dc29 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -25,7 +25,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -166,7 +166,7 @@ 
    Examples
    
 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-31 20:26:02.186012 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:46:02.256736 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Explore the data
 sce_layer
diff --git a/reference/frame_limits.html b/reference/frame_limits.html
index 8a81be94..9e0caa18 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -27,7 +27,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -154,7 +154,7 @@ 
    Examples
    
     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-10-31 20:26:04.315375 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:46:04.271249 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> $y_min
 #> [1] 64
 #> 
diff --git a/reference/gene_set_enrichment.html b/reference/gene_set_enrichment.html
index f68c5efb..2aecfdcd 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -22,7 +22,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -176,7 +176,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 20:26:20.646987 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-10 20:46:19.657173 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/gene_set_enrichment_plot.html b/reference/gene_set_enrichment_plot.html
index 36479f49..81e87fc3 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -178,7 +178,7 @@ 
    Examples
    
 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-10-31 20:26:22.286728 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-12-10 20:46:21.274062 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 ## Compute the gene set enrichment results
 asd_sfari_enrichment <- gene_set_enrichment(
diff --git a/reference/geom_spatial.html b/reference/geom_spatial.html
index aeaa0d8d..24e4b77e 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -20,7 +20,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
       
     
 
@@ -175,7 +175,7 @@ 
    Examples
    
     ## Clean up
     rm(spe_sub)
 }
-#> 2024-10-31 20:26:24.415304 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:46:23.365864 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
    diff --git a/reference/get_colors.html b/reference/get_colors.html index 6eb9c01a..e614fcb4 100644 --- a/reference/get_colors.html +++ b/reference/get_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -105,7 +105,7 @@

    Examples

    
 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-10-31 20:26:40.291074 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-12-10 20:46:42.011496 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Example layer colors with the corresponding names
 get_colors(libd_layer_colors, sce_layer$layer_guess)
diff --git a/reference/img_edit.html b/reference/img_edit.html
index 339041a6..9596b625 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.10
+        1.19.0
    @@ -222,7 +222,7 @@

    Examples

    x <- img_edit(spe, sampleid = "151507", brightness = 25) plot(x) } -#> 2024-10-31 20:26:41.819093 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:46:43.529951 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1     diff --git a/reference/img_update.html b/reference/img_update.html index 093c4979..8e1b09ab 100644 --- a/reference/img_update.html +++ b/reference/img_update.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -139,7 +139,7 @@

    Examples

    ## Reduce brightness to 25% and update the imgData() imgData(img_update(spe, sampleid = "151507", brightness = 25)) } -#> 2024-10-31 20:26:57.861005 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:46:59.800441 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 #> DataFrame with 13 rows and 4 columns #> sample_id image_id data scaleFactor #> <character> <character> <list> <numeric> diff --git a/reference/img_update_all.html b/reference/img_update_all.html index 1c2a7814..9ab6913a 100644 --- a/reference/img_update_all.html +++ b/reference/img_update_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -138,7 +138,7 @@

    Examples

    ## update the imgData() imgData(img_update_all(spe, brightness = 25)) } -#> 2024-10-31 20:27:12.503589 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:47:14.373615 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 #> DataFrame with 24 rows and 4 columns #> sample_id image_id data scaleFactor #> <character> <character> <list> <numeric> diff --git a/reference/index.html b/reference/index.html index 66b3f01b..57b8a753 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html index 24696286..d8d33e9c 100644 --- a/reference/layer_boxplot.html +++ b/reference/layer_boxplot.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -185,9 +185,9 @@

    Examples

    if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-31 20:27:29.766162 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-10 20:47:31.652485 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-31 20:27:30.976263 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:47:32.847935 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## Top 2 genes from the enrichment model sig_genes <- sig_genes_extract_all( diff --git a/reference/layer_matrix_plot.html b/reference/layer_matrix_plot.html index 5ed94fd1..6a04c042 100644 --- a/reference/layer_matrix_plot.html +++ b/reference/layer_matrix_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html index ef6d46b8..fd0ec8e4 100644 --- a/reference/layer_stat_cor.html +++ b/reference/layer_stat_cor.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -156,7 +156,7 @@

    Examples

    if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-31 20:27:34.95313 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-10 20:47:36.626619 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 ## Compute the correlations cor_stats_layer <- layer_stat_cor( diff --git a/reference/layer_stat_cor_plot.html b/reference/layer_stat_cor_plot.html index d9b87d7b..f2e6203e 100644 --- a/reference/layer_stat_cor_plot.html +++ b/reference/layer_stat_cor_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -145,7 +145,7 @@

    Examples

    if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-31 20:27:36.412057 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-10 20:47:38.040256 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 ## Compute the correlations cor_stats_layer <- layer_stat_cor( diff --git a/reference/libd_layer_colors.html b/reference/libd_layer_colors.html index 73977025..e64ca5e1 100644 --- a/reference/libd_layer_colors.html +++ b/reference/libd_layer_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/locate_images.html b/reference/locate_images.html index 838f5a0a..2adeba17 100644 --- a/reference/locate_images.html +++ b/reference/locate_images.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/multi_gene_pca.html b/reference/multi_gene_pca.html index f181e27c..513d24f2 100644 --- a/reference/multi_gene_pca.html +++ b/reference/multi_gene_pca.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/multi_gene_sparsity.html b/reference/multi_gene_sparsity.html index e70cafdb..80d177c9 100644 --- a/reference/multi_gene_sparsity.html +++ b/reference/multi_gene_sparsity.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/multi_gene_z_score.html b/reference/multi_gene_z_score.html index afc142d0..11640f6d 100644 --- a/reference/multi_gene_z_score.html +++ b/reference/multi_gene_z_score.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/prep_stitched_data.html b/reference/prep_stitched_data.html index 9bd9d287..a1f82808 100644 --- a/reference/prep_stitched_data.html +++ b/reference/prep_stitched_data.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/read10xVisiumAnalysis.html b/reference/read10xVisiumAnalysis.html index 520b252a..10ee9e33 100644 --- a/reference/read10xVisiumAnalysis.html +++ b/reference/read10xVisiumAnalysis.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/read10xVisiumWrapper.html b/reference/read10xVisiumWrapper.html index 8fb414ef..ae373716 100644 --- a/reference/read10xVisiumWrapper.html +++ b/reference/read10xVisiumWrapper.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html index 0741bbd7..737e9807 100644 --- a/reference/registration_block_cor.html +++ b/reference/registration_block_cor.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -146,9 +146,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 20:27:39.588807 make pseudobulk object -#> 2024-10-31 20:27:39.816979 drop lowly expressed genes -#> 2024-10-31 20:27:39.899263 normalize expression +#> 2024-12-10 20:47:41.061931 make pseudobulk object +#> 2024-12-10 20:47:41.26834 drop lowly expressed genes +#> 2024-12-10 20:47:41.335768 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -180,7 +180,7 @@

    Examples

    #> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-31 20:27:39.982418 create model matrix +#> 2024-12-10 20:47:41.412806 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -198,8 +198,8 @@

    Examples

    #> E_G0 0 20.97006 #> A_G1 0 19.18719 block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-31 20:27:39.995663 run duplicateCorrelation() -#> 2024-10-31 20:27:41.290589 The estimated correlation is: -0.0187869166526901 +#> 2024-12-10 20:47:41.425331 run duplicateCorrelation() +#> 2024-12-10 20:47:42.663303 The estimated correlation is: -0.0187869166526901     diff --git a/reference/registration_model.html b/reference/registration_model.html index 0afd0d8f..5760373b 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -148,9 +148,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 20:27:41.727388 make pseudobulk object -#> 2024-10-31 20:27:41.920928 drop lowly expressed genes -#> 2024-10-31 20:27:41.979309 normalize expression +#> 2024-12-10 20:47:43.086129 make pseudobulk object +#> 2024-12-10 20:47:43.270059 drop lowly expressed genes +#> 2024-12-10 20:47:43.323211 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -181,7 +181,7 @@

    Examples

    #> D_S S D 14 #> E_S S E 11 registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-31 20:27:42.054168 create model matrix +#> 2024-12-10 20:47:43.396329 create model matrix head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M #> A_G0 1 0 0 diff --git a/reference/registration_pseudobulk.html b/reference/registration_pseudobulk.html index 360b7739..0cfa6f4b 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -159,9 +159,9 @@

    Examples

    ## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 20:27:42.476538 make pseudobulk object -#> 2024-10-31 20:27:42.662947 drop lowly expressed genes -#> 2024-10-31 20:27:42.717835 normalize expression +#> 2024-12-10 20:47:43.804197 make pseudobulk object +#> 2024-12-10 20:47:43.983433 drop lowly expressed genes +#> 2024-12-10 20:47:44.039587 normalize expression colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns #> Mutation_Status Cell_Cycle Treatment sample_id age diff --git a/reference/registration_stats_anova.html b/reference/registration_stats_anova.html index 09ed71dd..13247eb1 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -180,9 +180,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 20:27:43.330647 make pseudobulk object -#> 2024-10-31 20:27:43.48633 drop lowly expressed genes -#> 2024-10-31 20:27:43.542063 normalize expression +#> 2024-12-10 20:47:44.609267 make pseudobulk object +#> 2024-12-10 20:47:44.761405 drop lowly expressed genes +#> 2024-12-10 20:47:44.814546 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -214,7 +214,7 @@

    Examples

    #> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-31 20:27:43.618136 create model matrix +#> 2024-12-10 20:47:44.886694 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -233,13 +233,13 @@

    Examples

    #> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-31 20:27:43.63019 run duplicateCorrelation() -#> 2024-10-31 20:27:44.946026 The estimated correlation is: -0.0187869166526901 +#> 2024-12-10 20:47:44.898148 run duplicateCorrelation() +#> 2024-12-10 20:47:46.157179 The estimated correlation is: -0.0187869166526901 results_anova <- registration_stats_anova(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-10-31 20:27:44.95863 computing F-statistics +#> 2024-12-10 20:47:46.169142 computing F-statistics head(results_anova) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1328075 0.93918553 0.9951876 5.499488 ENSG1 gene1 @@ -254,7 +254,7 @@

    Examples

    block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "example" ) -#> 2024-10-31 20:27:45.027015 computing F-statistics +#> 2024-12-10 20:47:46.230564 computing F-statistics head(results_anova_nan) #> f_stat_example p_value_example fdr_example AveExpr_example ensembl gene #> 1 0.1357180 0.93736053 0.9943765 5.499488 ENSG1 gene1 @@ -276,7 +276,7 @@

    Examples

    covars = NULL, gene_ensembl = "ensembl", gene_name = "gene_name", suffix = "nocovar" ) -#> 2024-10-31 20:27:45.077416 computing F-statistics +#> 2024-12-10 20:47:46.280049 computing F-statistics head(results_anova_nocovar) #> f_stat_nocovar p_value_nocovar fdr_nocovar AveExpr_nocovar ensembl gene #> 1 0.1393641 0.9351345 0.9962097 5.499488 ENSG1 gene1 diff --git a/reference/registration_stats_enrichment.html b/reference/registration_stats_enrichment.html index 7412d21f..08768448 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -171,9 +171,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 20:27:45.608077 make pseudobulk object -#> 2024-10-31 20:27:45.794401 drop lowly expressed genes -#> 2024-10-31 20:27:45.850316 normalize expression +#> 2024-12-10 20:47:46.793334 make pseudobulk object +#> 2024-12-10 20:47:46.969903 drop lowly expressed genes +#> 2024-12-10 20:47:47.02204 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -205,7 +205,7 @@

    Examples

    #> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-31 20:27:45.925474 create model matrix +#> 2024-12-10 20:47:47.097021 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -224,14 +224,14 @@

    Examples

    #> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-31 20:27:45.937309 run duplicateCorrelation() -#> 2024-10-31 20:27:47.229975 The estimated correlation is: -0.0187869166526901 +#> 2024-12-10 20:47:47.108299 run duplicateCorrelation() +#> 2024-12-10 20:47:48.339458 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-31 20:27:47.233631 computing enrichment statistics -#> 2024-10-31 20:27:47.352396 extract and reformat enrichment results +#> 2024-12-10 20:47:48.342894 computing enrichment statistics +#> 2024-12-10 20:47:48.457594 extract and reformat enrichment results head(results_enrichment) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1482017 0.5610669 -0.3612235 -0.3458508 0.88374480 0.58130631 @@ -260,8 +260,8 @@

    Examples

    block_cor = NaN, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-31 20:27:47.385547 computing enrichment statistics -#> 2024-10-31 20:27:47.488791 extract and reformat enrichment results +#> 2024-12-10 20:47:48.48979 computing enrichment statistics +#> 2024-12-10 20:47:48.593203 extract and reformat enrichment results head(results_enrichment_nan) #> t_stat_G0 t_stat_G1 t_stat_G2M t_stat_S p_value_G0 p_value_G1 #> Gene_0001 0.1497747 0.56711100 -0.3650801 -0.3495404 0.88252049 0.57727506 diff --git a/reference/registration_stats_pairwise.html b/reference/registration_stats_pairwise.html index 9fa962f5..bbee5690 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -173,9 +173,9 @@

    Examples

    #> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-10-31 20:27:47.96792 make pseudobulk object -#> 2024-10-31 20:27:48.129766 drop lowly expressed genes -#> 2024-10-31 20:27:48.183394 normalize expression +#> 2024-12-10 20:47:49.056688 make pseudobulk object +#> 2024-12-10 20:47:49.216398 drop lowly expressed genes +#> 2024-12-10 20:47:49.268796 normalize expression #> #> rgstr_> colData(sce_pseudo) #> DataFrame with 20 rows and 8 columns @@ -207,7 +207,7 @@

    Examples

    #> E_S S E 11 #> #> rgstr_> registration_mod <- registration_model(sce_pseudo, "age") -#> 2024-10-31 20:27:48.256356 create model matrix +#> 2024-12-10 20:47:49.341395 create model matrix #> #> rgstr_> head(registration_mod) #> registration_variableG0 registration_variableG1 registration_variableG2M @@ -226,14 +226,14 @@

    Examples

    #> A_G1 0 19.18719 #> #> rgst__> block_cor <- registration_block_cor(sce_pseudo, registration_mod) -#> 2024-10-31 20:27:48.267876 run duplicateCorrelation() -#> 2024-10-31 20:27:49.57912 The estimated correlation is: -0.0187869166526901 +#> 2024-12-10 20:47:49.352443 run duplicateCorrelation() +#> 2024-12-10 20:47:50.616924 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-31 20:27:49.58132 running the baseline pairwise model -#> 2024-10-31 20:27:49.598271 computing pairwise statistics +#> 2024-12-10 20:47:50.618752 running the baseline pairwise model +#> 2024-12-10 20:47:50.635284 computing pairwise statistics head(results_pairwise) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2393683 0.29771391 0.28880637 0.5370822 0.5281747 @@ -277,8 +277,8 @@

    Examples

    block_cor = NaN, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-10-31 20:27:49.663743 running the baseline pairwise model -#> 2024-10-31 20:27:49.681207 computing pairwise statistics +#> 2024-12-10 20:47:50.699803 running the baseline pairwise model +#> 2024-12-10 20:47:50.71706 computing pairwise statistics head(results_pairwise_nan) #> t_stat_G0-G1 t_stat_G0-G2M t_stat_G0-S t_stat_G1-G2M t_stat_G1-S #> Gene_0001 -0.2419770 0.30095840 0.29195379 0.5429354 0.5339308 diff --git a/reference/registration_wrapper.html b/reference/registration_wrapper.html index ab063d8a..e6b32bc4 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -205,18 +205,18 @@

    Examples

    gene_name = "gene_name", suffix = "wrapper" ) -#> 2024-10-31 20:27:50.212626 make pseudobulk object -#> 2024-10-31 20:27:50.362406 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-10-31 20:27:50.383501 drop lowly expressed genes -#> 2024-10-31 20:27:50.436933 normalize expression -#> 2024-10-31 20:27:50.494299 create model matrix -#> 2024-10-31 20:27:50.505118 run duplicateCorrelation() -#> 2024-10-31 20:27:52.985647 The estimated correlation is: -0.0783081238514532 -#> 2024-10-31 20:27:52.988182 computing enrichment statistics -#> 2024-10-31 20:27:53.104357 extract and reformat enrichment results -#> 2024-10-31 20:27:53.130206 running the baseline pairwise model -#> 2024-10-31 20:27:53.148322 computing pairwise statistics -#> 2024-10-31 20:27:53.223214 computing F-statistics +#> 2024-12-10 20:47:51.215556 make pseudobulk object +#> 2024-12-10 20:47:51.366816 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-12-10 20:47:51.38774 drop lowly expressed genes +#> 2024-12-10 20:47:51.439983 normalize expression +#> 2024-12-10 20:47:51.496244 create model matrix +#> 2024-12-10 20:47:51.506722 run duplicateCorrelation() +#> 2024-12-10 20:47:53.907525 The estimated correlation is: -0.0783081238514532 +#> 2024-12-10 20:47:53.909845 computing enrichment statistics +#> 2024-12-10 20:47:54.021204 extract and reformat enrichment results +#> 2024-12-10 20:47:54.046154 running the baseline pairwise model +#> 2024-12-10 20:47:54.064062 computing pairwise statistics +#> 2024-12-10 20:47:54.137443 computing F-statistics ## Explore the results from registration_wrapper() class(example_modeling_results) diff --git a/reference/run_app.html b/reference/run_app.html index f09c01c4..31ad0657 100644 --- a/reference/run_app.html +++ b/reference/run_app.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index f54cb73e..fbe43078 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -127,7 +127,7 @@

    Examples

    ## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-10-31 20:27:55.895246 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:47:56.62485 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/sig_genes_extract.html b/reference/sig_genes_extract.html index bfa8b528..60a65693 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -156,9 +156,9 @@

    Examples

    if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-31 20:28:09.439362 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-10 20:48:10.277804 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-31 20:28:10.657705 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:48:11.476472 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## anova top 10 genes sig_genes_extract( diff --git a/reference/sig_genes_extract_all.html b/reference/sig_genes_extract_all.html index dffecb88..24ac9629 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -128,9 +128,9 @@

    Examples

    if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-10-31 20:28:14.031199 loading file /github/home/.cache/R/BiocFileCache/4a1260aa093_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-12-10 20:48:14.004614 loading file /github/home/.cache/R/BiocFileCache/ff83f604882_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-10-31 20:28:15.238751 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:48:15.202765 loading file /github/home/.cache/R/BiocFileCache/ff8151ae68d_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 ## top 10 genes for all models sig_genes_extract_all( diff --git a/reference/sort_clusters.html b/reference/sort_clusters.html index 711ea2b1..5cccc3c7 100644 --- a/reference/sort_clusters.html +++ b/reference/sort_clusters.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/spatialLIBD-package.html b/reference/spatialLIBD-package.html index 2f172871..a342eff0 100644 --- a/reference/spatialLIBD-package.html +++ b/reference/spatialLIBD-package.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html index 09c9c8f2..d164cb88 100644 --- a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html +++ b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html @@ -23,7 +23,7 @@ spatialLIBD - 1.17.10 + 1.19.0 diff --git a/reference/vis_clus.html b/reference/vis_clus.html index efc1d7f1..b40c0704 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -242,7 +242,7 @@

    Examples

    ) print(p4) } -#> 2024-10-31 20:28:18.021968 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:48:18.076404 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_clus_p.html b/reference/vis_clus_p.html index eab18833..85db7b64 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -202,7 +202,7 @@

    Examples

    ## Clean up rm(spe_sub) } -#> 2024-10-31 20:28:37.921685 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:48:38.052489 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index e61a1628..baf9d85e 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -341,7 +341,7 @@

    Examples

    ) print(p8) } -#> 2024-10-31 20:28:53.312282 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:48:53.417166 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene_p.html b/reference/vis_gene_p.html index e977a387..2cb1e97b 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -215,7 +215,7 @@

    Examples

    ## Clean up rm(spe_sub) } -#> 2024-10-31 20:29:19.803842 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:49:19.154484 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_clus.html b/reference/vis_grid_clus.html index 4f9b6b92..e0034b86 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -237,7 +237,7 @@

    Examples

    ## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-10-31 20:29:35.17602 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:49:34.425672 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_grid_gene.html b/reference/vis_grid_gene.html index ce92d7dc..7395a0ab 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.10 + 1.19.0 @@ -256,7 +256,7 @@

    Examples

    ## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-10-31 20:29:51.87273 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-12-10 20:49:50.974002 loading file /github/home/.cache/R/BiocFileCache/1ac74ead0d1a_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1