From f3d14d4ec73ea9e8f13943783396807e1d5eb293 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Thu, 9 May 2024 15:17:49 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20LieberIn?= =?UTF-8?q?stitute/spatialLIBD@f25860feda852255423fe315fd99a13f0b0db6a8=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/TenX_data_download.html | 39 ++++++++------- articles/guide_to_spatial_registration.html | 51 ++++++++++---------- articles/multi_gene_plots.html | 35 +++++++------- articles/spatialLIBD.html | 48 +++++++++--------- authors.html | 18 +++---- pkgdown.yml | 2 +- reference/add_images.html | 26 +++++----- reference/add_key.html | 2 +- reference/annotate_registered_clusters.html | 2 +- reference/check_modeling_results.html | 2 +- reference/check_sce.html | 2 +- reference/check_sce_layer.html | 2 +- reference/check_spe.html | 2 +- reference/cluster_export.html | 2 +- reference/cluster_import.html | 6 +-- reference/fetch_data.html | 2 +- reference/frame_limits.html | 2 +- reference/gene_set_enrichment.html | 2 +- reference/gene_set_enrichment_plot.html | 2 +- reference/geom_spatial.html | 2 +- reference/get_colors.html | 2 +- reference/img_edit.html | 2 +- reference/img_update.html | 2 +- reference/img_update_all.html | 2 +- reference/layer_boxplot.html | 4 +- reference/layer_stat_cor.html | 2 +- reference/layer_stat_cor_plot.html | 2 +- reference/registration_block_cor.html | 12 ++--- reference/registration_model.html | 8 +-- reference/registration_pseudobulk.html | 6 +-- reference/registration_stats_anova.html | 18 +++---- reference/registration_stats_enrichment.html | 20 ++++---- reference/registration_stats_pairwise.html | 20 ++++---- reference/registration_wrapper.html | 24 ++++----- reference/sce_to_spe.html | 2 +- reference/sig_genes_extract.html | 4 +- reference/sig_genes_extract_all.html | 4 +- reference/vis_clus.html | 2 +- reference/vis_clus_p.html | 2 +- reference/vis_gene.html | 2 +- reference/vis_gene_p.html | 2 +- reference/vis_grid_clus.html | 2 +- reference/vis_grid_gene.html | 2 +- 43 files changed, 195 insertions(+), 200 deletions(-) diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 7f51663f..0f627e41 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -119,7 +119,7 @@

Leonardo University
-

3 May 2024

+

9 May 2024

Source: vignettes/TenX_data_download.Rmd @@ -201,12 +201,11 @@

Citing spatialLIBD#> B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, #> Ravichandran P, Tran MN, Seyedian A, Consortium P, Hyde TM, Kleinman #> JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, -#> Collado-Torres L, Maynard KR (2023). "Integrated single cell and -#> unsupervised spatial transcriptomic analysis defines molecular -#> anatomy of the human dorsolateral prefrontal cortex." _bioRxiv_. -#> doi:10.1101/2023.02.15.528722 -#> <https://doi.org/10.1101/2023.02.15.528722>, -#> <https://www.biorxiv.org/content/10.1101/2023.02.15.528722v1>. +#> Collado-Torres L, Maynard KR (2024). "A data-driven single-cell and +#> spatial transcriptomic map of the human prefrontal cortex." +#> _Science_. doi:10.1126/science.adh1938 +#> <https://doi.org/10.1126/science.adh1938>, +#> <https://doi.org/10.1126/science.adh1938>. #> #> Kwon SH, Parthiban S, Tippani M, Divecha HR, Eagles NJ, Lobana JS, #> Williams SR, Mark M, Bharadwaj RA, Kleinman JE, Hyde TM, Page SC, @@ -535,7 +534,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/d0b7e009959_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/1bc49c0bec4_gencode.v32.annotation.gtf.gz" ## Import into R (takes ~1 min) gtf <- rtracklayer::import(gtf_cache) @@ -821,11 +820,11 @@

Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE, reference_gtf = gtf_cache ) -#> 2024-05-03 14:30:58.735969 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger -#> 2024-05-03 14:31:10.271631 read10xVisiumAnalysis: reading analysis output from SpaceRanger -#> 2024-05-03 14:31:11.456743 add10xVisiumAnalysis: adding analysis output from SpaceRanger -#> 2024-05-03 14:31:11.70923 rtracklayer::import: reading the reference GTF file -#> 2024-05-03 14:31:38.7758 adding gene information to the SPE object +#> 2024-05-09 15:16:47.467879 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger +#> 2024-05-09 15:16:58.821311 read10xVisiumAnalysis: reading analysis output from SpaceRanger +#> 2024-05-09 15:16:59.851306 add10xVisiumAnalysis: adding analysis output from SpaceRanger +#> 2024-05-09 15:17:00.099717 rtracklayer::import: reading the reference GTF file +#> 2024-05-09 15:17:26.995151 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() @@ -833,7 +832,7 @@

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. -#> 2024-05-03 14:31:40.293049 adding information used by spatialLIBD +#> 2024-05-09 15:17:28.54866 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1117,9 +1116,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-05-03 14:31:41 UTC"
+
#> [1] "2024-05-09 15:17:29 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.781 mins
+
#> Time difference of 1.777 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1131,7 +1130,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-05-03
+#>  date     2024-05-09
 #>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -1150,7 +1149,7 @@ 
Reproducibility#>  BiocFileCache          * 2.10.2      2024-03-27 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocGenerics           * 0.48.1      2023-11-01 [1] Bioconductor
 #>  BiocIO                   1.12.0      2023-10-24 [1] Bioconductor
-#>  BiocManager              1.30.22     2023-08-08 [2] CRAN (R 4.3.3)
+#>  BiocManager              1.30.22     2023-08-08 [1] RSPM (R 4.3.0)
 #>  BiocNeighbors            1.20.2      2024-01-07 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocParallel             1.36.0      2023-10-24 [1] Bioconductor
 #>  BiocSingular             1.18.0      2023-10-24 [1] Bioconductor
@@ -1193,7 +1192,7 @@ 
Reproducibility#>  fields                   15.2        2023-08-17 [1] RSPM (R 4.3.0)
 #>  filelock                 1.0.3       2023-12-11 [1] RSPM (R 4.3.0)
 #>  foreach                  1.5.2       2022-02-02 [1] RSPM (R 4.3.0)
-#>  fs                       1.6.4       2024-04-25 [2] RSPM (R 4.3.0)
+#>  fs                       1.6.3       2023-07-20 [2] RSPM (R 4.3.0)
 #>  generics                 0.1.3       2022-07-05 [1] RSPM (R 4.3.0)
 #>  GenomeInfoDb           * 1.38.8      2024-03-15 [1] Bioconductor 3.18 (R 4.3.2)
 #>  GenomeInfoDbData         1.2.11      2024-04-06 [1] Bioconductor
@@ -1285,7 +1284,7 @@ 
Reproducibility#>  SparseArray              1.2.4       2024-02-11 [1] Bioconductor 3.18 (R 4.3.2)
 #>  sparseMatrixStats        1.14.0      2023-10-24 [1] Bioconductor
 #>  SpatialExperiment      * 1.12.0      2023-10-24 [1] Bioconductor
-#>  spatialLIBD            * 1.17.0      2024-05-03 [1] Bioconductor
+#>  spatialLIBD            * 1.17.0      2024-05-09 [1] Bioconductor
 #>  statmod                  1.5.0       2023-01-06 [1] RSPM (R 4.3.0)
 #>  stringi                  1.8.3       2023-12-11 [2] RSPM (R 4.3.0)
 #>  stringr                  1.5.1       2023-11-14 [2] RSPM (R 4.3.0)
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index c34d3648..c0534f02 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -103,7 +103,7 @@ 
Louise
 Development

       
                   
-            
3 May 2024

+            
9 May 2024

       
       Source: vignettes/guide_to_spatial_registration.Rmd
       
@@ -226,12 +226,11 @@ 
Citing spatialLIBD#>   B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB,
 #>   Ravichandran P, Tran MN, Seyedian A, Consortium P, Hyde TM, Kleinman
 #>   JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K,
-#>   Collado-Torres L, Maynard KR (2023). "Integrated single cell and
-#>   unsupervised spatial transcriptomic analysis defines molecular
-#>   anatomy of the human dorsolateral prefrontal cortex." _bioRxiv_.
-#>   doi:10.1101/2023.02.15.528722
-#>   <https://doi.org/10.1101/2023.02.15.528722>,
-#>   <https://www.biorxiv.org/content/10.1101/2023.02.15.528722v1>.
+#>   Collado-Torres L, Maynard KR (2024). "A data-driven single-cell and
+#>   spatial transcriptomic map of the human prefrontal cortex."
+#>   _Science_. doi:10.1126/science.adh1938
+#>   <https://doi.org/10.1126/science.adh1938>,
+#>   <https://doi.org/10.1126/science.adh1938>.
 #> 
 #>   Kwon SH, Parthiban S, Tippani M, Divecha HR, Eagles NJ, Lobana JS,
 #>   Williams SR, Mark M, Bharadwaj RA, Kleinman JE, Hyde TM, Page SC,
@@ -287,7 +286,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-05-03 14:28:00.784261 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-09 15:13:47.870231 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_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
@@ -389,18 +388,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-05-03 14:28:08.595304 make pseudobulk object
-#> 2024-05-03 14:28:10.256402 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-05-03 14:28:10.315382 drop lowly expressed genes
-#> 2024-05-03 14:28:10.493234 normalize expression
-#> 2024-05-03 14:28:11.981613 create model matrix
-#> 2024-05-03 14:28:12.005035 run duplicateCorrelation()
-#> 2024-05-03 14:28:25.510119 The estimated correlation is: 0.138734774807097
-#> 2024-05-03 14:28:25.512728 computing enrichment statistics
-#> 2024-05-03 14:28:26.653336 extract and reformat enrichment results
-#> 2024-05-03 14:28:26.705633 running the baseline pairwise model
-#> 2024-05-03 14:28:26.883332 computing pairwise statistics
-#> 2024-05-03 14:28:28.220459 computing F-statistics

+#> 2024-05-09 15:13:55.602064 make pseudobulk object
+#> 2024-05-09 15:13:57.303033 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
+#> 2024-05-09 15:13:57.365153 drop lowly expressed genes
+#> 2024-05-09 15:13:57.545492 normalize expression
+#> 2024-05-09 15:13:59.030571 create model matrix
+#> 2024-05-09 15:13:59.05476 run duplicateCorrelation()
+#> 2024-05-09 15:14:12.730844 The estimated correlation is: 0.138734774807097
+#> 2024-05-09 15:14:12.733469 computing enrichment statistics
+#> 2024-05-09 15:14:13.910157 extract and reformat enrichment results
+#> 2024-05-09 15:14:13.963411 running the baseline pairwise model
+#> 2024-05-09 15:14:14.126265 computing pairwise statistics
+#> 2024-05-09 15:14:15.465982 computing F-statistics

Extract Enrichment t-statistics @@ -560,9 +559,9 @@

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

Date the vignette was generated.

-
#> [1] "2024-05-03 14:28:29 UTC"
+
#> [1] "2024-05-09 15:14:16 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 41.516 secs
+
#> Time difference of 41.891 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -574,7 +573,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-05-03
+#>  date     2024-05-09
 #>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -593,7 +592,7 @@ 
Reproducibility#>  BiocFileCache            2.10.2      2024-03-27 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocGenerics           * 0.48.1      2023-11-01 [1] Bioconductor
 #>  BiocIO                   1.12.0      2023-10-24 [1] Bioconductor
-#>  BiocManager              1.30.22     2023-08-08 [2] CRAN (R 4.3.3)
+#>  BiocManager              1.30.22     2023-08-08 [1] RSPM (R 4.3.0)
 #>  BiocNeighbors            1.20.2      2024-01-07 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocParallel             1.36.0      2023-10-24 [1] Bioconductor
 #>  BiocSingular             1.18.0      2023-10-24 [1] Bioconductor
@@ -633,7 +632,7 @@ 
Reproducibility#>  fields                   15.2        2023-08-17 [1] RSPM (R 4.3.0)
 #>  filelock                 1.0.3       2023-12-11 [1] RSPM (R 4.3.0)
 #>  foreach                  1.5.2       2022-02-02 [1] RSPM (R 4.3.0)
-#>  fs                       1.6.4       2024-04-25 [2] RSPM (R 4.3.0)
+#>  fs                       1.6.3       2023-07-20 [2] RSPM (R 4.3.0)
 #>  generics                 0.1.3       2022-07-05 [1] RSPM (R 4.3.0)
 #>  GenomeInfoDb           * 1.38.8      2024-03-15 [1] Bioconductor 3.18 (R 4.3.2)
 #>  GenomeInfoDbData         1.2.11      2024-04-06 [1] Bioconductor
@@ -715,7 +714,7 @@ 
Reproducibility#>  SparseArray              1.2.4       2024-02-11 [1] Bioconductor 3.18 (R 4.3.2)
 #>  sparseMatrixStats        1.14.0      2023-10-24 [1] Bioconductor
 #>  SpatialExperiment      * 1.12.0      2023-10-24 [1] Bioconductor
-#>  spatialLIBD            * 1.17.0      2024-05-03 [1] Bioconductor
+#>  spatialLIBD            * 1.17.0      2024-05-09 [1] Bioconductor
 #>  statmod                  1.5.0       2023-01-06 [1] RSPM (R 4.3.0)
 #>  stringi                  1.8.3       2023-12-11 [2] RSPM (R 4.3.0)
 #>  stringr                  1.5.1       2023-11-14 [2] RSPM (R 4.3.0)
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 90b7ca6d..dd8126d4 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -110,7 +110,7 @@ 
Leonardo
 Public Health

       
                   
-            
3 May 2024

+            
9 May 2024

       
       Source: vignettes/multi_gene_plots.Rmd
       
@@ -135,7 +135,7 @@ 
3 May 2024

 prefrontal cortex (DLPFC) (Huuki-Myers, Spangler, Eagles, Montgomergy,
 Kwon, Guo, Grant-Peters, Divecha, Tippani, Sriworarat, Nguyen,
 Ravichandran, Tran, Seyedian, Consortium, Hyde, Kleinman, Battle, Page,
-Ryten, Hicks, Martinowich, Collado-Torres, and Maynard, 2023).

+Ryten, Hicks, Martinowich, Collado-Torres, and Maynard, 2024).

 
 library("spatialLIBD")
 spe <- fetch_data(type = "spatialDLPFC_Visium_example_subset")
@@ -197,9 +197,9 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-05-03 14:28:53.698954 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-09 15:14:41.419183 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-05-03 14:28:54.590285 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:14:42.239849 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 sig_genes <- sig_genes_extract_all(
     n = 400,
     modeling_results = modeling_results,
@@ -391,7 +391,7 @@ 
Visualizing non-gene continuo
 colData(spe) along with actual genes. We can combine for
 example the expression of GFAP, which is a known astrocyte
 marker gene, with the spot deconvolution results for astrocytes computed
-using Tangram (Huuki-Myers, Spangler, Eagles et al., 2023).

+using Tangram (Huuki-Myers, Spangler, Eagles et al., 2024).

 
 vis_gene(
     spe,
@@ -423,9 +423,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-05-03 14:29:10 UTC"

+
#> [1] "2024-05-09 15:14:58 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 37.144 secs

+
#> Time difference of 37.442 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -437,7 +437,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-05-03
+#>  date     2024-05-09
 #>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -456,7 +456,7 @@ 
Reproducibility#>  BiocFileCache            2.10.2      2024-03-27 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocGenerics           * 0.48.1      2023-11-01 [1] Bioconductor
 #>  BiocIO                   1.12.0      2023-10-24 [1] Bioconductor
-#>  BiocManager              1.30.22     2023-08-08 [2] CRAN (R 4.3.3)
+#>  BiocManager              1.30.22     2023-08-08 [1] RSPM (R 4.3.0)
 #>  BiocNeighbors            1.20.2      2024-01-07 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocParallel             1.36.0      2023-10-24 [1] Bioconductor
 #>  BiocSingular             1.18.0      2023-10-24 [1] Bioconductor
@@ -497,7 +497,7 @@ 
Reproducibility#>  fields                   15.2        2023-08-17 [1] RSPM (R 4.3.0)
 #>  filelock                 1.0.3       2023-12-11 [1] RSPM (R 4.3.0)
 #>  foreach                  1.5.2       2022-02-02 [1] RSPM (R 4.3.0)
-#>  fs                       1.6.4       2024-04-25 [2] RSPM (R 4.3.0)
+#>  fs                       1.6.3       2023-07-20 [2] RSPM (R 4.3.0)
 #>  generics                 0.1.3       2022-07-05 [1] RSPM (R 4.3.0)
 #>  GenomeInfoDb           * 1.38.8      2024-03-15 [1] Bioconductor 3.18 (R 4.3.2)
 #>  GenomeInfoDbData         1.2.11      2024-04-06 [1] Bioconductor
@@ -580,7 +580,7 @@ 
Reproducibility#>  SparseArray              1.2.4       2024-02-11 [1] Bioconductor 3.18 (R 4.3.2)
 #>  sparseMatrixStats        1.14.0      2023-10-24 [1] Bioconductor
 #>  SpatialExperiment      * 1.12.0      2023-10-24 [1] Bioconductor
-#>  spatialLIBD            * 1.17.0      2024-05-03 [1] Bioconductor
+#>  spatialLIBD            * 1.17.0      2024-05-09 [1] Bioconductor
 #>  statmod                  1.5.0       2023-01-06 [1] RSPM (R 4.3.0)
 #>  stringi                  1.8.3       2023-12-11 [2] RSPM (R 4.3.0)
 #>  stringr                  1.5.1       2023-11-14 [2] RSPM (R 4.3.0)
@@ -628,14 +628,13 @@ 
Bibliographyhttps://github.com/rstudio/rmarkdown.
 

 

-[2]
-L. A. Huuki-Myers, A. Spangler, N. J. Eagles, et al. “Integrated single
-cell and unsupervised spatial transcriptomic analysis defines molecular
-anatomy of the human dorsolateral prefrontal cortex”. In:
-bioRxiv (2023). DOI:
-10.1101/2023.02.15.528722.
+[2]
+L. A. Huuki-Myers, A. Spangler, N. J. Eagles, et al. “A data-driven
+single-cell and spatial transcriptomic map of the human prefrontal
+cortex”. In: Science (2024). DOI:
+10.1126/science.adh1938.
 URL:
-https://www.biorxiv.org/content/10.1101/2023.02.15.528722v1.
+https://doi.org/10.1126/science.adh1938.
 

 

 [3]
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 8f88cec8..7da2164b 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -116,7 +116,7 @@ 
Andrew E.
 Campus

       
                   
-            
3 May 2024

+            
9 May 2024

       
       Source: vignettes/spatialLIBD.Rmd
       
@@ -289,12 +289,11 @@ 
Citing spatialLIBD#>   B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB,
 #>   Ravichandran P, Tran MN, Seyedian A, Consortium P, Hyde TM, Kleinman
 #>   JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K,
-#>   Collado-Torres L, Maynard KR (2023). "Integrated single cell and
-#>   unsupervised spatial transcriptomic analysis defines molecular
-#>   anatomy of the human dorsolateral prefrontal cortex." _bioRxiv_.
-#>   doi:10.1101/2023.02.15.528722
-#>   <https://doi.org/10.1101/2023.02.15.528722>,
-#>   <https://www.biorxiv.org/content/10.1101/2023.02.15.528722v1>.
+#>   Collado-Torres L, Maynard KR (2024). "A data-driven single-cell and
+#>   spatial transcriptomic map of the human prefrontal cortex."
+#>   _Science_. doi:10.1126/science.adh1938
+#>   <https://doi.org/10.1126/science.adh1938>,
+#>   <https://doi.org/10.1126/science.adh1938>.
 #> 
 #>   Kwon SH, Parthiban S, Tippani M, Divecha HR, Eagles NJ, Lobana JS,
 #>   Williams SR, Mark M, Bharadwaj RA, Kleinman JE, Hyde TM, Page SC,
@@ -417,7 +416,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-05-03 14:29:27.182347 loading file /github/home/.cache/R/BiocFileCache/d0b62d21a29_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-05-09 15:15:14.927314 loading file /github/home/.cache/R/BiocFileCache/1bc41643124_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
 spe <- sce_to_spe(sce)
@@ -429,9 +428,9 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-05-03 14:29:31.774464 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:15:19.972899 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-05-03 14:29:32.284214 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-05-09 15:15:20.417555 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

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

 
@@ -504,7 +503,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>  10.160   0.433  10.603
+#>  10.354   0.416  10.787
 
 ## Explore the result
 class(sig_genes)
@@ -1166,7 +1165,7 @@ 
spatialDLPFChttp://research.libd.org/spatialDLPFC/ for more
+Maynard, 2024). See http://research.libd.org/spatialDLPFC/ for more
 information about this project.

 
See the Twitter thread 🧵 below for a brief overview of the #spatialDLPFC
 project.

@@ -1380,9 +1379,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

 
Date the vignette was generated.

-
#> [1] "2024-05-03 14:29:50 UTC"

+
#> [1] "2024-05-09 15:15:38 UTC"

 
Wallclock time spent generating the vignette.

-
#> Time difference of 36.281 secs

+
#> Time difference of 36.857 secs

 
R session information.

 
#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1394,7 +1393,7 @@ 
Reproducibility#>  collate  en_US.UTF-8
 #>  ctype    en_US.UTF-8
 #>  tz       UTC
-#>  date     2024-05-03
+#>  date     2024-05-09
 #>  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 #> 
 #> ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
@@ -1413,7 +1412,7 @@ 
Reproducibility#>  BiocFileCache            2.10.2      2024-03-27 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocGenerics           * 0.48.1      2023-11-01 [1] Bioconductor
 #>  BiocIO                   1.12.0      2023-10-24 [1] Bioconductor
-#>  BiocManager              1.30.22     2023-08-08 [2] CRAN (R 4.3.3)
+#>  BiocManager              1.30.22     2023-08-08 [1] RSPM (R 4.3.0)
 #>  BiocNeighbors            1.20.2      2024-01-07 [1] Bioconductor 3.18 (R 4.3.2)
 #>  BiocParallel             1.36.0      2023-10-24 [1] Bioconductor
 #>  BiocSingular             1.18.0      2023-10-24 [1] Bioconductor
@@ -1454,7 +1453,7 @@ 
Reproducibility#>  fields                   15.2        2023-08-17 [1] RSPM (R 4.3.0)
 #>  filelock                 1.0.3       2023-12-11 [1] RSPM (R 4.3.0)
 #>  foreach                  1.5.2       2022-02-02 [1] RSPM (R 4.3.0)
-#>  fs                       1.6.4       2024-04-25 [2] RSPM (R 4.3.0)
+#>  fs                       1.6.3       2023-07-20 [2] RSPM (R 4.3.0)
 #>  generics                 0.1.3       2022-07-05 [1] RSPM (R 4.3.0)
 #>  GenomeInfoDb           * 1.38.8      2024-03-15 [1] Bioconductor 3.18 (R 4.3.2)
 #>  GenomeInfoDbData         1.2.11      2024-04-06 [1] Bioconductor
@@ -1537,7 +1536,7 @@ 
Reproducibility#>  SparseArray              1.2.4       2024-02-11 [1] Bioconductor 3.18 (R 4.3.2)
 #>  sparseMatrixStats        1.14.0      2023-10-24 [1] Bioconductor
 #>  SpatialExperiment      * 1.12.0      2023-10-24 [1] Bioconductor
-#>  spatialLIBD            * 1.17.0      2024-05-03 [1] Bioconductor
+#>  spatialLIBD            * 1.17.0      2024-05-09 [1] Bioconductor
 #>  statmod                  1.5.0       2023-01-06 [1] RSPM (R 4.3.0)
 #>  stringi                  1.8.3       2023-12-11 [2] RSPM (R 4.3.0)
 #>  stringr                  1.5.1       2023-11-14 [2] RSPM (R 4.3.0)
@@ -1643,14 +1642,13 @@ 
Bibliographyhttp://www.nature.com/nmeth/journal/v12/n2/full/nmeth.3252.html.
 

 

-[11]
-L. A. Huuki-Myers, A. Spangler, N. J. Eagles, et al. “Integrated single
-cell and unsupervised spatial transcriptomic analysis defines molecular
-anatomy of the human dorsolateral prefrontal cortex”. In:
-bioRxiv (2023). DOI:
-10.1101/2023.02.15.528722.
+[11]
+L. A. Huuki-Myers, A. Spangler, N. J. Eagles, et al. “A data-driven
+single-cell and spatial transcriptomic map of the human prefrontal
+cortex”. In: Science (2024). DOI:
+10.1126/science.adh1938.
 URL:
-https://www.biorxiv.org/content/10.1101/2023.02.15.528722v1.
+https://doi.org/10.1126/science.adh1938.
 

 

 [12]
diff --git a/authors.html b/authors.html
index 2c5a0c9e..c2b3269d 100644
--- a/authors.html
+++ b/authors.html
@@ -138,18 +138,18 @@ 
Citation

   doi = {10.1038/s41593-020-00787-0},
   url = {https://www.nature.com/articles/s41593-020-00787-0},
 }

-    
Huuki-Myers LA, Spangler A, Eagles NJ, Montgomergy KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, Consortium P, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR (2023).
-“Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex.”
-bioRxiv.
-doi:10.1101/2023.02.15.528722, https://www.biorxiv.org/content/10.1101/2023.02.15.528722v1. 
+    
Huuki-Myers LA, Spangler A, Eagles NJ, Montgomergy KD, Kwon SH, Guo B, Grant-Peters M, Divecha HR, Tippani M, Sriworarat C, Nguyen AB, Ravichandran P, Tran MN, Seyedian A, Consortium P, Hyde TM, Kleinman JE, Battle A, Page SC, Ryten M, Hicks SC, Martinowich K, Collado-Torres L, Maynard KR (2024).
+“A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex.”
+Science.
+doi:10.1126/science.adh1938, https://doi.org/10.1126/science.adh1938. 
 

     
@Article{,
-  title = {Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex},
+  title = {A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex},
   author = {Louise A. Huuki-Myers and Abby Spangler and Nicholas J. Eagles and Kelsey D. Montgomergy and Sang Ho Kwon and Boyi Guo and Melissa Grant-Peters and Heena R. Divecha and Madhavi Tippani and Chaichontat Sriworarat and Annie B. Nguyen and Prashanthi Ravichandran and Matthew N. Tran and Arta Seyedian and PsychENCODE Consortium and Thomas M. Hyde and Joel E. Kleinman and Alexis Battle and Stephanie C. Page and Mina Ryten and Stephanie C. Hicks and Keri Martinowich and Leonardo Collado-Torres and Kristen R. Maynard},
-  year = {2023},
-  journal = {bioRxiv},
-  doi = {10.1101/2023.02.15.528722},
-  url = {https://www.biorxiv.org/content/10.1101/2023.02.15.528722v1},
+  year = {2024},
+  journal = {Science},
+  doi = {10.1126/science.adh1938},
+  url = {https://doi.org/10.1126/science.adh1938},
 }

     
Kwon SH, Parthiban S, Tippani M, Divecha HR, Eagles NJ, Lobana JS, Williams SR, Mark M, Bharadwaj RA, Kleinman JE, Hyde TM, Page SC, Hicks SC, Martinowich K, Maynard KR, Collado-Torres L (2023).
 “Influence of Alzheimer’s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex.”
diff --git a/pkgdown.yml b/pkgdown.yml
index 68932a65..a3a06691 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -6,5 +6,5 @@ articles:
   multi_gene_plots: multi_gene_plots.html
   spatialLIBD: spatialLIBD.html
   TenX_data_download: TenX_data_download.html
-last_built: 2024-05-03T14:22Z
+last_built: 2024-05-09T15:07Z
 
diff --git a/reference/add_images.html b/reference/add_images.html
index bc725621..12ac510d 100644
--- a/reference/add_images.html
+++ b/reference/add_images.html
@@ -165,29 +165,29 @@ 
Examples

         image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png")
     ))
 }
-#> 2024-05-03 14:22:27.800351 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
-#> 2024-05-03 14:22:44.289698 adding image for sample 151507
-#> 2024-05-03 14:22:45.345304 adding image for sample 151508
+#> 2024-05-09 15:08:14.821414 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:08:30.482315 adding image for sample 151507
+#> 2024-05-09 15:08:31.41007 adding image for sample 151508
 #> Warning: No image was found for sample: 151508
-#> 2024-05-03 14:22:45.345625 adding image for sample 151509
+#> 2024-05-09 15:08:31.410397 adding image for sample 151509
 #> Warning: No image was found for sample: 151509
-#> 2024-05-03 14:22:45.345836 adding image for sample 151510
+#> 2024-05-09 15:08:31.41061 adding image for sample 151510
 #> Warning: No image was found for sample: 151510
-#> 2024-05-03 14:22:45.346044 adding image for sample 151669
+#> 2024-05-09 15:08:31.41081 adding image for sample 151669
 #> Warning: No image was found for sample: 151669
-#> 2024-05-03 14:22:45.346246 adding image for sample 151670
+#> 2024-05-09 15:08:31.411011 adding image for sample 151670
 #> Warning: No image was found for sample: 151670
-#> 2024-05-03 14:22:45.346437 adding image for sample 151671
+#> 2024-05-09 15:08:31.411205 adding image for sample 151671
 #> Warning: No image was found for sample: 151671
-#> 2024-05-03 14:22:45.346629 adding image for sample 151672
+#> 2024-05-09 15:08:31.411396 adding image for sample 151672
 #> Warning: No image was found for sample: 151672
-#> 2024-05-03 14:22:45.346818 adding image for sample 151673
+#> 2024-05-09 15:08:31.411588 adding image for sample 151673
 #> Warning: No image was found for sample: 151673
-#> 2024-05-03 14:22:45.34701 adding image for sample 151674
+#> 2024-05-09 15:08:31.411783 adding image for sample 151674
 #> Warning: No image was found for sample: 151674
-#> 2024-05-03 14:22:45.347203 adding image for sample 151675
+#> 2024-05-09 15:08:31.411972 adding image for sample 151675
 #> Warning: No image was found for sample: 151675
-#> 2024-05-03 14:22:45.347393 adding image for sample 151676
+#> 2024-05-09 15:08:31.412163 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 494bbd93..22f23d31 100644
--- a/reference/add_key.html
+++ b/reference/add_key.html
@@ -117,7 +117,7 @@ 
Examples

     ## Note that the original 'key' order was 'sample_id'_'barcode' and we'
     ## have since changed it to 'barcode'_'sample_id'.
 }
-#> 2024-05-03 14:22:47.925328 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:08:33.900334 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> [1] "AAACAACGAATAGTTC-1_151507" "AAACAAGTATCTCCCA-1_151507"
 #> [3] "AAACAATCTACTAGCA-1_151507" "AAACACCAATAACTGC-1_151507"
 #> [5] "AAACAGCTTTCAGAAG-1_151507" "AAACAGGGTCTATATT-1_151507"
diff --git a/reference/annotate_registered_clusters.html b/reference/annotate_registered_clusters.html
index d0c249d5..804e7f88 100644
--- a/reference/annotate_registered_clusters.html
+++ b/reference/annotate_registered_clusters.html
@@ -139,7 +139,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-05-03 14:23:02.214292 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-09 15:08:48.124699 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_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 14d690ce..1dfd41a7 100644
--- a/reference/check_modeling_results.html
+++ b/reference/check_modeling_results.html
@@ -108,7 +108,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-05-03 14:23:03.233251 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-09 15:08:49.192367 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_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 b53d337a..c2bba0b6 100644
--- a/reference/check_sce.html
+++ b/reference/check_sce.html
@@ -131,7 +131,7 @@ 
Examples

     ## Check the object
     check_sce(sce_example)
 }
-#> 2024-05-03 14:23:04.285563 loading file /github/home/.cache/R/BiocFileCache/d0b62d21a29_sce_sub_for_vignette.Rdata%3Fdl%3D1
+#> 2024-05-09 15:08:50.272649 loading file /github/home/.cache/R/BiocFileCache/1bc41643124_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 2e6381e2..14866139 100644
--- a/reference/check_sce_layer.html
+++ b/reference/check_sce_layer.html
@@ -111,7 +111,7 @@ 
Examples

     

 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-05-03 14:23:06.632889 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:08:52.721595 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
 
 ## Check the object
 check_sce_layer(sce_layer)
diff --git a/reference/check_spe.html b/reference/check_spe.html
index d5471522..8c5d21af 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -123,7 +123,7 @@ 
Examples

     ## Check the object
     check_spe(spe)
 }
-#> 2024-05-03 14:23:07.85953 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:08:53.943111 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 a655dea3..cb51f841 100644
--- a/reference/cluster_export.html
+++ b/reference/cluster_export.html
@@ -134,7 +134,7 @@ 
Examples

     cluster_export(spe, "spatialLIBD")
     cluster_export(spe, "GraphBased")
 }
-#> 2024-05-03 14:23:23.280077 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:09:09.474272 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 20c61b84..36098d3a 100644
--- a/reference/cluster_import.html
+++ b/reference/cluster_import.html
@@ -137,11 +137,11 @@ 
Examples

     ## Re-import them
     colData(cluster_import(spe))
 }
-#> 2024-05-03 14:23:37.698689 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:09:23.82443 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmppi3OOu/exported_clusters/spatialLIBD' already exists
+#> Warning: '/tmp/Rtmp178Sq2/exported_clusters/spatialLIBD' already exists
 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it.
-#> Warning: '/tmp/Rtmppi3OOu/exported_clusters/GraphBased' already exists
+#> Warning: '/tmp/Rtmp178Sq2/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/fetch_data.html b/reference/fetch_data.html
index 8fe170d1..21f128c3 100644
--- a/reference/fetch_data.html
+++ b/reference/fetch_data.html
@@ -165,7 +165,7 @@ 
Examples

 ## Download the SingleCellExperiment object
 ## at the layer-level
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-05-03 14:23:52.992785 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:09:39.093723 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_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 aa9a5bbd..bacc5182 100644
--- a/reference/frame_limits.html
+++ b/reference/frame_limits.html
@@ -154,7 +154,7 @@ 
Examples

     ## Obtain the frame limits for one sample
     frame_limits(spe, sampleid = "151673")
 }
-#> 2024-05-03 14:23:54.749425 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:09:40.691844 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 4acbf406..cf699d5e 100644
--- a/reference/gene_set_enrichment.html
+++ b/reference/gene_set_enrichment.html
@@ -176,7 +176,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-05-03 14:24:09.005948 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-09 15:09:55.014095 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_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 269b5bb6..db28a0ee 100644
--- a/reference/gene_set_enrichment_plot.html
+++ b/reference/gene_set_enrichment_plot.html
@@ -178,7 +178,7 @@ 
Examples

 if (!exists("modeling_results")) {
     modeling_results <- fetch_data(type = "modeling_results")
 }
-#> 2024-05-03 14:24:10.327382 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-09 15:09:56.347061 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_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 27e52623..9a3e2861 100644
--- a/reference/geom_spatial.html
+++ b/reference/geom_spatial.html
@@ -175,7 +175,7 @@ 
Examples

     ## Clean up
     rm(spe_sub)
 }
-#> 2024-05-03 14:24:12.229863 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:09:58.069715 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/get_colors.html b/reference/get_colors.html index 64db23ea..2f5b7ec7 100644 --- a/reference/get_colors.html +++ b/reference/get_colors.html @@ -105,7 +105,7 @@

Examples


 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-05-03 14:24:27.494662 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:10:14.183197 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_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 f2d8b2d9..f11f314d 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -222,7 +222,7 @@ 
Examples

     x <- img_edit(spe, sampleid = "151507", brightness = 25)
     plot(x)
 }
-#> 2024-05-03 14:24:28.666993 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-09 15:10:15.404807 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
diff --git a/reference/img_update.html b/reference/img_update.html index 2bfac377..427e6f44 100644 --- a/reference/img_update.html +++ b/reference/img_update.html @@ -139,7 +139,7 @@

Examples

## Reduce brightness to 25% and update the imgData() imgData(img_update(spe, sampleid = "151507", brightness = 25)) } -#> 2024-05-03 14:24:44.3686 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:10:30.913979 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 020d7348..4118c19f 100644 --- a/reference/img_update_all.html +++ b/reference/img_update_all.html @@ -138,7 +138,7 @@

Examples

## update the imgData() imgData(img_update_all(spe, brightness = 25)) } -#> 2024-05-03 14:24:58.467992 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:10:45.087581 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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/layer_boxplot.html b/reference/layer_boxplot.html index 74edfdde..26c622a9 100644 --- a/reference/layer_boxplot.html +++ b/reference/layer_boxplot.html @@ -185,9 +185,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-03 14:25:15.07182 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:01.93517 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-03 14:25:15.981738 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:02.876447 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_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_stat_cor.html b/reference/layer_stat_cor.html index c98142c0..d0540cf3 100644 --- a/reference/layer_stat_cor.html +++ b/reference/layer_stat_cor.html @@ -156,7 +156,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-03 14:25:19.402976 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:06.380349 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_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 e7c0968a..b9307261 100644 --- a/reference/layer_stat_cor_plot.html +++ b/reference/layer_stat_cor_plot.html @@ -145,7 +145,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-03 14:25:20.470103 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:07.470443 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 ## Compute the correlations cor_stats_layer <- layer_stat_cor( diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html index ac73e41e..bfede8ca 100644 --- a/reference/registration_block_cor.html +++ b/reference/registration_block_cor.html @@ -146,9 +146,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-03 14:25:23.520841 make pseudobulk object -#> 2024-05-03 14:25:23.710559 drop lowly expressed genes -#> 2024-05-03 14:25:23.780748 normalize expression +#> 2024-05-09 15:11:10.572097 make pseudobulk object +#> 2024-05-09 15:11:10.770819 drop lowly expressed genes +#> 2024-05-09 15:11:10.842599 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") -#> 2024-05-03 14:25:23.858798 create model matrix +#> 2024-05-09 15:11:10.922137 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) -#> 2024-05-03 14:25:23.8716 run duplicateCorrelation() -#> 2024-05-03 14:25:25.239626 The estimated correlation is: -0.0187869166526901 +#> 2024-05-09 15:11:10.934844 run duplicateCorrelation() +#> 2024-05-09 15:11:12.303912 The estimated correlation is: -0.0187869166526901 diff --git a/reference/registration_model.html b/reference/registration_model.html index c6058fe6..a0689b0d 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -148,9 +148,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-03 14:25:25.663107 make pseudobulk object -#> 2024-05-03 14:25:25.850625 drop lowly expressed genes -#> 2024-05-03 14:25:25.905114 normalize expression +#> 2024-05-09 15:11:12.734682 make pseudobulk object +#> 2024-05-09 15:11:12.92834 drop lowly expressed genes +#> 2024-05-09 15:11:12.985913 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") -#> 2024-05-03 14:25:25.97927 create model matrix +#> 2024-05-09 15:11:13.062282 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 5c471981..942021dd 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -159,9 +159,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-03 14:25:26.44373 make pseudobulk object -#> 2024-05-03 14:25:26.597517 drop lowly expressed genes -#> 2024-05-03 14:25:26.651151 normalize expression +#> 2024-05-09 15:11:13.527166 make pseudobulk object +#> 2024-05-09 15:11:13.684158 drop lowly expressed genes +#> 2024-05-09 15:11:13.738271 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 a7022fe6..55197043 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -180,9 +180,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-03 14:25:27.247002 make pseudobulk object -#> 2024-05-03 14:25:27.402889 drop lowly expressed genes -#> 2024-05-03 14:25:27.495944 normalize expression +#> 2024-05-09 15:11:14.354697 make pseudobulk object +#> 2024-05-09 15:11:14.514566 drop lowly expressed genes +#> 2024-05-09 15:11:14.596318 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") -#> 2024-05-03 14:25:27.57008 create model matrix +#> 2024-05-09 15:11:14.672328 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) -#> 2024-05-03 14:25:27.581064 run duplicateCorrelation() -#> 2024-05-03 14:25:28.885649 The estimated correlation is: -0.0187869166526901 +#> 2024-05-09 15:11:14.683241 run duplicateCorrelation() +#> 2024-05-09 15:11:15.977854 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" ) -#> 2024-05-03 14:25:28.898071 computing F-statistics +#> 2024-05-09 15:11:15.990202 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" ) -#> 2024-05-03 14:25:28.961572 computing F-statistics +#> 2024-05-09 15:11:16.054018 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" ) -#> 2024-05-03 14:25:29.011328 computing F-statistics +#> 2024-05-09 15:11:16.104376 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 5713f420..58eda38a 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -171,9 +171,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-03 14:25:29.561758 make pseudobulk object -#> 2024-05-03 14:25:29.750419 drop lowly expressed genes -#> 2024-05-03 14:25:29.805427 normalize expression +#> 2024-05-09 15:11:16.655692 make pseudobulk object +#> 2024-05-09 15:11:16.846749 drop lowly expressed genes +#> 2024-05-09 15:11:16.900823 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") -#> 2024-05-03 14:25:29.879403 create model matrix +#> 2024-05-09 15:11:16.975043 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) -#> 2024-05-03 14:25:29.890396 run duplicateCorrelation() -#> 2024-05-03 14:25:31.187294 The estimated correlation is: -0.0187869166526901 +#> 2024-05-09 15:11:16.986019 run duplicateCorrelation() +#> 2024-05-09 15:11:18.288608 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-05-03 14:25:31.191031 computing enrichment statistics -#> 2024-05-03 14:25:31.306759 extract and reformat enrichment results +#> 2024-05-09 15:11:18.292403 computing enrichment statistics +#> 2024-05-09 15:11:18.413057 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" ) -#> 2024-05-03 14:25:31.339784 computing enrichment statistics -#> 2024-05-03 14:25:31.441903 extract and reformat enrichment results +#> 2024-05-09 15:11:18.447105 computing enrichment statistics +#> 2024-05-09 15:11:18.552893 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 045c21b1..45c6978a 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -173,9 +173,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-03 14:25:31.918126 make pseudobulk object -#> 2024-05-03 14:25:32.104103 drop lowly expressed genes -#> 2024-05-03 14:25:32.158174 normalize expression +#> 2024-05-09 15:11:19.037328 make pseudobulk object +#> 2024-05-09 15:11:19.226588 drop lowly expressed genes +#> 2024-05-09 15:11:19.281738 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") -#> 2024-05-03 14:25:32.231661 create model matrix +#> 2024-05-09 15:11:19.356305 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) -#> 2024-05-03 14:25:32.242673 run duplicateCorrelation() -#> 2024-05-03 14:25:33.546865 The estimated correlation is: -0.0187869166526901 +#> 2024-05-09 15:11:19.367417 run duplicateCorrelation() +#> 2024-05-09 15:11:20.670746 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-05-03 14:25:33.548897 running the baseline pairwise model -#> 2024-05-03 14:25:33.565392 computing pairwise statistics +#> 2024-05-09 15:11:20.672792 running the baseline pairwise model +#> 2024-05-09 15:11:20.689609 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" ) -#> 2024-05-03 14:25:33.63393 running the baseline pairwise model -#> 2024-05-03 14:25:33.651188 computing pairwise statistics +#> 2024-05-09 15:11:20.756824 running the baseline pairwise model +#> 2024-05-09 15:11:20.774626 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 c345c8d5..b42aefbd 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -200,18 +200,18 @@

Examples

sce, "Cell_Cycle", "sample_id", c("age"), "ensembl", "gene_name", "wrapper" ) -#> 2024-05-03 14:25:34.209103 make pseudobulk object -#> 2024-05-03 14:25:34.361217 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-05-03 14:25:34.382151 drop lowly expressed genes -#> 2024-05-03 14:25:34.435952 normalize expression -#> 2024-05-03 14:25:34.493232 create model matrix -#> 2024-05-03 14:25:34.50384 run duplicateCorrelation() -#> 2024-05-03 14:25:36.954731 The estimated correlation is: -0.0783081238514532 -#> 2024-05-03 14:25:36.956989 computing enrichment statistics -#> 2024-05-03 14:25:37.071104 extract and reformat enrichment results -#> 2024-05-03 14:25:37.096178 running the baseline pairwise model -#> 2024-05-03 14:25:37.113797 computing pairwise statistics -#> 2024-05-03 14:25:37.186999 computing F-statistics +#> 2024-05-09 15:11:21.338129 make pseudobulk object +#> 2024-05-09 15:11:21.49547 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-05-09 15:11:21.516572 drop lowly expressed genes +#> 2024-05-09 15:11:21.569838 normalize expression +#> 2024-05-09 15:11:21.626992 create model matrix +#> 2024-05-09 15:11:21.637284 run duplicateCorrelation() +#> 2024-05-09 15:11:24.10187 The estimated correlation is: -0.0783081238514532 +#> 2024-05-09 15:11:24.104105 computing enrichment statistics +#> 2024-05-09 15:11:24.221802 extract and reformat enrichment results +#> 2024-05-09 15:11:24.24661 running the baseline pairwise model +#> 2024-05-09 15:11:24.26474 computing pairwise statistics +#> 2024-05-09 15:11:24.338662 computing F-statistics diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 00f31830..d5ca61ee 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-05-03 14:25:38.76718 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:26.26534 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 179f3cf5..a4ff9848 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -156,9 +156,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-03 14:25:51.847758 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:39.401601 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-03 14:25:52.710114 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:40.291023 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_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 ddbb002b..b4a114fc 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -128,9 +128,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-03 14:25:57.081001 loading file /github/home/.cache/R/BiocFileCache/d0b17ec1af6_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:44.74062 loading file /github/home/.cache/R/BiocFileCache/1bc2678f16e_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-03 14:25:58.02132 loading file /github/home/.cache/R/BiocFileCache/d0b5d104e05_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:45.548888 loading file /github/home/.cache/R/BiocFileCache/1bc556ec2b2_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/vis_clus.html b/reference/vis_clus.html index c119a0af..0b376cd0 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -232,7 +232,7 @@

Examples

) print(p4) } -#> 2024-05-03 14:26:00.407209 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:11:47.723342 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 b97c5c4d..6b68d327 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-05-03 14:26:19.724599 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:12:07.237182 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index c5556062..966c4858 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -331,7 +331,7 @@

Examples

) print(p8) } -#> 2024-05-03 14:26:34.650533 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:12:22.199168 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 1c7de86c..b7b8eca3 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -220,7 +220,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-05-03 14:27:00.845141 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:12:48.268878 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 11d525cf..3731090c 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -227,7 +227,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-05-03 14:27:15.766448 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:13:03.071764 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_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 5ddf9dee..1dbe171b 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -246,7 +246,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-05-03 14:27:32.11435 loading file /github/home/.cache/R/BiocFileCache/177f585de710_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-09 15:13:19.426742 loading file /github/home/.cache/R/BiocFileCache/c306ef1eb68_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1