diff --git a/404.html b/404.html index 60b6a20e..884d9458 100644 --- a/404.html +++ b/404.html @@ -40,7 +40,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index 86e85def..1dd5adfe 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html index 8b7d2b93..2cf9dbf7 100644 --- a/CONTRIBUTING.html +++ b/CONTRIBUTING.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/SUPPORT.html b/SUPPORT.html index 4a557758..5ca03f67 100644 --- a/SUPPORT.html +++ b/SUPPORT.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/articles/TenX_data_download.html b/articles/TenX_data_download.html index 7c376f72..b94f41d1 100644 --- a/articles/TenX_data_download.html +++ b/articles/TenX_data_download.html @@ -41,7 +41,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -212,9 +212,9 @@

Citing spatialLIBD#> 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." _bioRxiv_. doi:10.1101/2023.04.20.537710 -#> <https://doi.org/10.1101/2023.04.20.537710>, -#> <https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1>. +#> cortex." _GEN Biotechnology_. doi:10.1089/genbio.2023.0019 +#> <https://doi.org/10.1089/genbio.2023.0019>, +#> <https://doi.org/10.1089/genbio.2023.0019>. #> #> To see these entries in BibTeX format, use 'print(<citation>, #> bibtex=TRUE)', 'toBibtex(.)', or set @@ -538,7 +538,7 @@

From Gencode## Show the GTF cache location gtf_cache #> BFC4 -#> "/github/home/.cache/R/BiocFileCache/272603ecd3b_gencode.v32.annotation.gtf.gz" +#> "/github/home/.cache/R/BiocFileCache/2e77eb20d92_gencode.v32.annotation.gtf.gz" 
 
 ## Import into R (takes ~1 min)
@@ -832,11 +832,11 @@ 
Wrapper functions= c("lowres", "hires", "detected", "aligned"), load = TRUE,
     reference_gtf = gtf_cache
 )
-#> 2024-05-24 06:38:38.834715 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
-#> 2024-05-24 06:38:49.341463 read10xVisiumAnalysis: reading analysis output from SpaceRanger
-#> 2024-05-24 06:38:50.315964 add10xVisiumAnalysis: adding analysis output from SpaceRanger
-#> 2024-05-24 06:38:50.555229 rtracklayer::import: reading the reference GTF file
-#> 2024-05-24 06:39:16.039132 adding gene information to the SPE object
+#> 2024-05-24 18:17:42.424774 SpatialExperiment::read10xVisium: reading basic data from SpaceRanger
+#> 2024-05-24 18:17:53.135004 read10xVisiumAnalysis: reading analysis output from SpaceRanger
+#> 2024-05-24 18:17:54.141153 add10xVisiumAnalysis: adding analysis output from SpaceRanger
+#> 2024-05-24 18:17:54.384614 rtracklayer::import: reading the reference GTF file
+#> 2024-05-24 18:18:19.647692 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()
@@ -844,7 +844,7 @@ 
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.
-#> 2024-05-24 06:39:17.472739 adding information used by spatialLIBD
+#> 2024-05-24 18:18:21.106961 adding information used by spatialLIBD 
 ## Run our shiny app
 if (interactive()) {
@@ -1128,9 +1128,9 @@ 
Reproducibilitylibrary("knitr")
 knit("TenX_data_download.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-05-24 06:39:18 UTC"
+
#> [1] "2024-05-24 18:18:22 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 1.689 mins
+
#> Time difference of 1.687 mins

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1151,7 +1151,7 @@ 
Reproducibility#>  AnnotationDbi          1.66.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 #>  AnnotationHub          3.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  attempt                0.3.1       2020-05-03 [1] CRAN (R 4.4.0)
-#>  backports              1.4.1       2021-12-13 [1] CRAN (R 4.4.0)
+#>  backports              1.5.0       2024-05-23 [1] RSPM (R 4.4.0)
 #>  beachmat               2.20.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  beeswarm               0.4.0       2021-06-01 [1] CRAN (R 4.4.0)
 #>  benchmarkme            1.0.8       2022-06-12 [1] CRAN (R 4.4.0)
@@ -1295,7 +1295,7 @@ 
Reproducibility#>  SparseArray            1.4.5       2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 #>  sparseMatrixStats      1.16.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  SpatialExperiment    * 1.14.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
-#>  spatialLIBD          * 1.17.1      2024-05-24 [1] Bioconductor
+#>  spatialLIBD          * 1.17.2      2024-05-24 [1] Bioconductor
 #>  statmod                1.5.0       2023-01-06 [1] CRAN (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)
diff --git a/articles/guide_to_spatial_registration.html b/articles/guide_to_spatial_registration.html
index 1a2daeee..7329078a 100644
--- a/articles/guide_to_spatial_registration.html
+++ b/articles/guide_to_spatial_registration.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.17.1
+        1.17.2
       
     
 
@@ -237,9 +237,9 @@ 
Citing spatialLIBD#>   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." _bioRxiv_. doi:10.1101/2023.04.20.537710
-#>   <https://doi.org/10.1101/2023.04.20.537710>,
-#>   <https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1>.
+#>   cortex." _GEN Biotechnology_. doi:10.1089/genbio.2023.0019
+#>   <https://doi.org/10.1089/genbio.2023.0019>,
+#>   <https://doi.org/10.1089/genbio.2023.0019>.
 #> 
 #> To see these entries in BibTeX format, use 'print(<citation>,
 #> bibtex=TRUE)', 'toBibtex(.)', or set
@@ -286,7 +286,7 @@ 
Spatial Reference
 ## get reference layer enrichment statistics
 layer_modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-05-24 06:35:47.047988 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-05-24 18:14:48.392373 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 
 layer_modeling_results$enrichment[1:5, 1:5]
@@ -389,18 +389,18 @@ 
Get Enrichment statistics
     gene_ensembl = "gene_id",
     gene_name = "gene_name"
 )
-#> 2024-05-24 06:35:55.431226 make pseudobulk object
-#> 2024-05-24 06:35:57.076661 dropping 13 pseudo-bulked samples that are below 'min_ncells'.
-#> 2024-05-24 06:35:57.133294 drop lowly expressed genes
-#> 2024-05-24 06:35:57.293617 normalize expression
-#> 2024-05-24 06:35:58.019479 create model matrix
-#> 2024-05-24 06:35:58.043371 run duplicateCorrelation()
-#> 2024-05-24 06:36:11.79821 The estimated correlation is: 0.138734774807097
-#> 2024-05-24 06:36:11.800817 computing enrichment statistics
-#> 2024-05-24 06:36:12.902637 extract and reformat enrichment results
-#> 2024-05-24 06:36:12.957636 running the baseline pairwise model
-#> 2024-05-24 06:36:13.119462 computing pairwise statistics
-#> 2024-05-24 06:36:14.444971 computing F-statistics
+#> 2024-05-24 18:14:56.773553 make pseudobulk object +#> 2024-05-24 18:14:58.436308 dropping 13 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-05-24 18:14:58.493284 drop lowly expressed genes +#> 2024-05-24 18:14:58.650946 normalize expression +#> 2024-05-24 18:14:59.372174 create model matrix +#> 2024-05-24 18:14:59.396198 run duplicateCorrelation() +#> 2024-05-24 18:15:13.137674 The estimated correlation is: 0.138734774807097 +#> 2024-05-24 18:15:13.140286 computing enrichment statistics +#> 2024-05-24 18:15:14.202193 extract and reformat enrichment results +#> 2024-05-24 18:15:14.2576 running the baseline pairwise model +#> 2024-05-24 18:15:14.417956 computing pairwise statistics +#> 2024-05-24 18:15:15.732432 computing F-statistics

Extract Enrichment t-statistics @@ -561,9 +561,9 @@

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

Date the vignette was generated.

-
#> [1] "2024-05-24 06:36:15 UTC"
+
#> [1] "2024-05-24 18:15:16 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 40.343 secs
+
#> Time difference of 40.776 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -584,7 +584,7 @@ 
Reproducibility#>  AnnotationDbi          1.66.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 #>  AnnotationHub          3.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  attempt                0.3.1       2020-05-03 [1] CRAN (R 4.4.0)
-#>  backports              1.4.1       2021-12-13 [1] CRAN (R 4.4.0)
+#>  backports              1.5.0       2024-05-23 [1] RSPM (R 4.4.0)
 #>  beachmat               2.20.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  beeswarm               0.4.0       2021-06-01 [1] CRAN (R 4.4.0)
 #>  benchmarkme            1.0.8       2022-06-12 [1] CRAN (R 4.4.0)
@@ -715,7 +715,7 @@ 
Reproducibility#>  SparseArray            1.4.5       2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 #>  sparseMatrixStats      1.16.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  SpatialExperiment    * 1.14.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
-#>  spatialLIBD          * 1.17.1      2024-05-24 [1] Bioconductor
+#>  spatialLIBD          * 1.17.2      2024-05-24 [1] Bioconductor
 #>  statmod                1.5.0       2023-01-06 [1] CRAN (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)
diff --git a/articles/index.html b/articles/index.html
index b2aa84ee..697392e2 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.1
+        1.17.2
       
     
 
diff --git a/articles/multi_gene_plots.html b/articles/multi_gene_plots.html
index 63b1dc90..92373e35 100644
--- a/articles/multi_gene_plots.html
+++ b/articles/multi_gene_plots.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.17.1
+        1.17.2
       
     
 
@@ -197,10 +197,10 @@ 
Plotting One Gene
 modeling_results <- fetch_data(type = "modeling_results")
-#> 2024-05-24 06:36:38.7652 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

+#> 2024-05-24 18:15:41.328155 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
 sce_layer <- fetch_data(type = "sce_layer")
-#> 2024-05-24 06:36:39.654834 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 18:15:42.52693 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 
 sig_genes <- sig_genes_extract_all(
     n = 400,
@@ -426,9 +426,9 @@ 
Reproducibilitylibrary("knitr")
 knit("multi_gene_plots.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-05-24 06:36:55 UTC"
+
#> [1] "2024-05-24 18:15:58 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 36.694 secs
+
#> Time difference of 37.87 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -449,7 +449,7 @@ 
Reproducibility#>  AnnotationDbi          1.66.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 #>  AnnotationHub          3.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  attempt                0.3.1       2020-05-03 [1] CRAN (R 4.4.0)
-#>  backports              1.4.1       2021-12-13 [1] CRAN (R 4.4.0)
+#>  backports              1.5.0       2024-05-23 [1] RSPM (R 4.4.0)
 #>  beachmat               2.20.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  beeswarm               0.4.0       2021-06-01 [1] CRAN (R 4.4.0)
 #>  benchmarkme            1.0.8       2022-06-12 [1] CRAN (R 4.4.0)
@@ -582,7 +582,7 @@ 
Reproducibility#>  SparseArray            1.4.5       2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 #>  sparseMatrixStats      1.16.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  SpatialExperiment    * 1.14.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
-#>  spatialLIBD          * 1.17.1      2024-05-24 [1] Bioconductor
+#>  spatialLIBD          * 1.17.2      2024-05-24 [1] Bioconductor
 #>  statmod                1.5.0       2023-01-06 [1] CRAN (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)
diff --git a/articles/spatialLIBD.html b/articles/spatialLIBD.html
index 7d4fc649..3128ecd2 100644
--- a/articles/spatialLIBD.html
+++ b/articles/spatialLIBD.html
@@ -41,7 +41,7 @@
       
       
         spatialLIBD
-        1.17.1
+        1.17.2
       
     
 
@@ -300,9 +300,9 @@ 
Citing spatialLIBD#>   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." _bioRxiv_. doi:10.1101/2023.04.20.537710
-#>   <https://doi.org/10.1101/2023.04.20.537710>,
-#>   <https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1>.
+#>   cortex." _GEN Biotechnology_. doi:10.1089/genbio.2023.0019
+#>   <https://doi.org/10.1089/genbio.2023.0019>,
+#>   <https://doi.org/10.1089/genbio.2023.0019>.
 #> 
 #> To see these entries in BibTeX format, use 'print(<citation>,
 #> bibtex=TRUE)', 'toBibtex(.)', or set
@@ -416,7 +416,7 @@ 
Downloading the data with s
 
 ## Download the small example sce data
 sce <- fetch_data(type = "sce_example", eh = ehub)
-#> 2024-05-24 06:37:10.851743 loading file /github/home/.cache/R/BiocFileCache/2724577c975_sce_sub_for_vignette.Rdata%3Fdl%3D1

+#> 2024-05-24 18:16:14.374847 loading file /github/home/.cache/R/BiocFileCache/2e733fba06f_sce_sub_for_vignette.Rdata%3Fdl%3D1
 
 ## Convert to a SpatialExperiment object
@@ -429,10 +429,10 @@ 
Downloading the data with s
 
 ## Query ExperimentHub and download the data
 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer", eh = ehub)
-#> 2024-05-24 06:37:15.078541 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 18:16:18.900597 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 
 modeling_results <- fetch_data("modeling_results", eh = ehub)
-#> 2024-05-24 06:37:15.54428 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1
+#> 2024-05-24 18:16:19.367097 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1

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

@@ -509,7 +509,7 @@ 
Downloading the data with s
         )
 )
 #>    user  system elapsed 
-#>   9.311   0.272   9.616
+#> 9.071 0.404 9.498 
 
 ## Explore the result
@@ -1393,9 +1393,9 @@ 
Reproducibilitylibrary("knitr")
 knit("spatialLIBD.Rmd", tangle = TRUE)

Date the vignette was generated.

-
#> [1] "2024-05-24 06:37:33 UTC"
+
#> [1] "2024-05-24 18:16:36 UTC"

Wallclock time spent generating the vignette.

-
#> Time difference of 34.326 secs
+
#> Time difference of 35.144 secs

R session information.

#> ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 #>  setting  value
@@ -1416,7 +1416,7 @@ 
Reproducibility#>  AnnotationDbi          1.66.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
 #>  AnnotationHub          3.12.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  attempt                0.3.1       2020-05-03 [1] CRAN (R 4.4.0)
-#>  backports              1.4.1       2021-12-13 [1] CRAN (R 4.4.0)
+#>  backports              1.5.0       2024-05-23 [1] RSPM (R 4.4.0)
 #>  beachmat               2.20.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  beeswarm               0.4.0       2021-06-01 [1] CRAN (R 4.4.0)
 #>  benchmarkme            1.0.8       2022-06-12 [1] CRAN (R 4.4.0)
@@ -1549,7 +1549,7 @@ 
Reproducibility#>  SparseArray            1.4.5       2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
 #>  sparseMatrixStats      1.16.0      2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
 #>  SpatialExperiment    * 1.14.0      2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
-#>  spatialLIBD          * 1.17.1      2024-05-24 [1] Bioconductor
+#>  spatialLIBD          * 1.17.2      2024-05-24 [1] Bioconductor
 #>  statmod                1.5.0       2023-01-06 [1] CRAN (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)
@@ -1682,11 +1682,11 @@ 
Bibliography[14]
 S. H. Kwon, S. Parthiban, M. Tippani, et al. “Influence of Alzheimer’s
 disease related neuropathology on local microenvironment gene expression
-in the human inferior temporal cortex”. In: bioRxiv (2023).
-DOI:
-10.1101/2023.04.20.537710.
+in the human inferior temporal cortex”. In: GEN Biotechnology
+(2023). DOI:
+10.1089/genbio.2023.0019.
 URL:
-https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1.
+https://doi.org/10.1089/genbio.2023.0019.
 

 

 [15]
diff --git a/authors.html b/authors.html
index 0fdcf802..8da764a7 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         spatialLIBD
-        1.17.1
+        1.17.2
       
     
 
@@ -153,16 +153,16 @@ 
Citation

 }

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.” -bioRxiv. -doi:10.1101/2023.04.20.537710, https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1. +GEN Biotechnology. +doi:10.1089/genbio.2023.0019, https://doi.org/10.1089/genbio.2023.0019. 

@Article{,
   title = {Influence of Alzheimer’s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex},
   author = {Sang Ho Kwon and Sowmya Parthiban and Madhavi Tippani and Heena R. Divecha and Nicholas J. Eagles and Jashandeep S. Lobana and Stephen R. Williams and Michelle Mark and Rahul A. Bharadwaj and Joel E. Kleinman and Thomas M. Hyde and Stephanie C. Page and Stephanie C. Hicks and Keri Martinowich and Kristen R. Maynard and Leonardo Collado-Torres},
   year = {2023},
-  journal = {bioRxiv},
-  doi = {10.1101/2023.04.20.537710},
-  url = {https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1},
+  journal = {GEN Biotechnology},
+  doi = {10.1089/genbio.2023.0019},
+  url = {https://doi.org/10.1089/genbio.2023.0019},
 }
diff --git a/index.html b/index.html index d1306761..5a2cd1e5 100644 --- a/index.html +++ b/index.html @@ -41,7 +41,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -444,9 +444,9 @@

Citation#> 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." _bioRxiv_. doi:10.1101/2023.04.20.537710 -#> <https://doi.org/10.1101/2023.04.20.537710>, -#> <https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1>. +#> cortex." _GEN Biotechnology_. doi:10.1089/genbio.2023.0019 +#> <https://doi.org/10.1089/genbio.2023.0019>, +#> <https://doi.org/10.1089/genbio.2023.0019>. #> #> A BibTeX entry for LaTeX users is #> @@ -454,9 +454,9 @@

Citation#> title = {Influence of Alzheimer’s disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex}, #> author = {Sang Ho Kwon and Sowmya Parthiban and Madhavi Tippani and Heena R. Divecha and Nicholas J. Eagles and Jashandeep S. Lobana and Stephen R. Williams and Michelle Mark and Rahul A. Bharadwaj and Joel E. Kleinman and Thomas M. Hyde and Stephanie C. Page and Stephanie C. Hicks and Keri Martinowich and Kristen R. Maynard and Leonardo Collado-Torres}, #> year = {2023}, -#> journal = {bioRxiv}, -#> doi = {10.1101/2023.04.20.537710}, -#> url = {https://www.biorxiv.org/content/10.1101/2023.04.20.537710v1}, +#> journal = {GEN Biotechnology}, +#> doi = {10.1089/genbio.2023.0019}, +#> url = {https://doi.org/10.1089/genbio.2023.0019}, #> }

Please note that the spatialLIBD was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

diff --git a/news/index.html b/news/index.html index 23dfc22d..df381f9d 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/pkgdown.yml b/pkgdown.yml index 5f7a468f..7785e8f5 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: 2024-05-24T06:30Z +last_built: 2024-05-24T18:08Z diff --git a/reference/add10xVisiumAnalysis.html b/reference/add10xVisiumAnalysis.html index 3b75be62..94104463 100644 --- a/reference/add10xVisiumAnalysis.html +++ b/reference/add10xVisiumAnalysis.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/add_images.html b/reference/add_images.html index 388045f4..a74eaee5 100644 --- a/reference/add_images.html +++ b/reference/add_images.html @@ -25,7 +25,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -165,29 +165,29 @@

Examples

image_paths = c("151507" = "https://spatial-dlpfc.s3.us-east-2.amazonaws.com/images/151507_tissue_lowres_image.png") )) } -#> 2024-05-24 06:30:16.330822 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 -#> 2024-05-24 06:30:31.752493 adding image for sample 151507 -#> 2024-05-24 06:30:32.539664 adding image for sample 151508 +#> 2024-05-24 18:08:57.971147 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:09:13.5952 adding image for sample 151507 +#> 2024-05-24 18:09:15.204928 adding image for sample 151508 #> Warning: No image was found for sample: 151508 -#> 2024-05-24 06:30:32.539975 adding image for sample 151509 +#> 2024-05-24 18:09:15.205243 adding image for sample 151509 #> Warning: No image was found for sample: 151509 -#> 2024-05-24 06:30:32.540186 adding image for sample 151510 +#> 2024-05-24 18:09:15.205453 adding image for sample 151510 #> Warning: No image was found for sample: 151510 -#> 2024-05-24 06:30:32.540384 adding image for sample 151669 +#> 2024-05-24 18:09:15.205657 adding image for sample 151669 #> Warning: No image was found for sample: 151669 -#> 2024-05-24 06:30:32.540574 adding image for sample 151670 +#> 2024-05-24 18:09:15.205848 adding image for sample 151670 #> Warning: No image was found for sample: 151670 -#> 2024-05-24 06:30:32.540765 adding image for sample 151671 +#> 2024-05-24 18:09:15.206041 adding image for sample 151671 #> Warning: No image was found for sample: 151671 -#> 2024-05-24 06:30:32.540953 adding image for sample 151672 +#> 2024-05-24 18:09:15.206231 adding image for sample 151672 #> Warning: No image was found for sample: 151672 -#> 2024-05-24 06:30:32.54114 adding image for sample 151673 +#> 2024-05-24 18:09:15.206419 adding image for sample 151673 #> Warning: No image was found for sample: 151673 -#> 2024-05-24 06:30:32.541329 adding image for sample 151674 +#> 2024-05-24 18:09:15.206607 adding image for sample 151674 #> Warning: No image was found for sample: 151674 -#> 2024-05-24 06:30:32.541521 adding image for sample 151675 +#> 2024-05-24 18:09:15.206796 adding image for sample 151675 #> Warning: No image was found for sample: 151675 -#> 2024-05-24 06:30:32.541736 adding image for sample 151676 +#> 2024-05-24 18:09:15.206983 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 b3d9bf49..a6eeeb56 100644 --- a/reference/add_key.html +++ b/reference/add_key.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -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'. } -#> 2024-05-24 06:30:34.808823 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:09:17.852924 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 eec7513d..400e69b0 100644 --- a/reference/annotate_registered_clusters.html +++ b/reference/annotate_registered_clusters.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -139,7 +139,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:30:49.018547 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:09:32.751507 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_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 d64a35c8..71779f23 100644 --- a/reference/check_modeling_results.html +++ b/reference/check_modeling_results.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -108,7 +108,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:30:50.116349 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:09:34.173769 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_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 35deb302..57b81c23 100644 --- a/reference/check_sce.html +++ b/reference/check_sce.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -131,7 +131,7 @@

Examples

## Check the object check_sce(sce_example) } -#> 2024-05-24 06:30:51.164432 loading file /github/home/.cache/R/BiocFileCache/2724577c975_sce_sub_for_vignette.Rdata%3Fdl%3D1 +#> 2024-05-24 18:09:35.532856 loading file /github/home/.cache/R/BiocFileCache/2e733fba06f_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 8e337e69..e1d4a775 100644 --- a/reference/check_sce_layer.html +++ b/reference/check_sce_layer.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -111,7 +111,7 @@

Examples


 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-05-24 06:30:53.653019 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 18:09:38.402522 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_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 fb50748b..cc02663b 100644
--- a/reference/check_spe.html
+++ b/reference/check_spe.html
@@ -18,7 +18,7 @@
       
       
         spatialLIBD
-        1.17.1
+        1.17.2
@@ -123,7 +123,7 @@

Examples

## Check the object check_spe(spe) } -#> 2024-05-24 06:30:54.787223 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:09:39.872161 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 0314d5e3..801e4220 100644 --- a/reference/cluster_export.html +++ b/reference/cluster_export.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -134,7 +134,7 @@

Examples

cluster_export(spe, "spatialLIBD") cluster_export(spe, "GraphBased") } -#> 2024-05-24 06:31:09.85279 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:09:55.649224 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 5efc14df..75ffb6b6 100644 --- a/reference/cluster_import.html +++ b/reference/cluster_import.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -137,11 +137,11 @@

Examples

## Re-import them colData(cluster_import(spe)) } -#> 2024-05-24 06:31:24.282307 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:10:10.462122 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it. -#> Warning: '/tmp/RtmpQX6o9B/exported_clusters/spatialLIBD' already exists +#> Warning: '/tmp/RtmpXdatHk/exported_clusters/spatialLIBD' already exists #> Overwriting 'spe$key'. Set 'overwrite = FALSE' if you do not want to overwrite it. -#> Warning: '/tmp/RtmpQX6o9B/exported_clusters/GraphBased' already exists +#> Warning: '/tmp/RtmpXdatHk/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 a0aae87f..c9945870 100644 --- a/reference/enough_ram.html +++ b/reference/enough_ram.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/fetch_data.html b/reference/fetch_data.html index 5519970a..73167699 100644 --- a/reference/fetch_data.html +++ b/reference/fetch_data.html @@ -25,7 +25,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -165,7 +165,7 @@

Examples

## Download the SingleCellExperiment object ## at the layer-level if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer") -#> 2024-05-24 06:31:39.567145 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:10:26.583771 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_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 286e6f50..bc7c2d78 100644 --- a/reference/frame_limits.html +++ b/reference/frame_limits.html @@ -27,7 +27,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -154,7 +154,7 @@

Examples

## Obtain the frame limits for one sample frame_limits(spe, sampleid = "151673") } -#> 2024-05-24 06:31:41.17375 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:10:28.676734 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 bf36d8fe..dac2043d 100644 --- a/reference/gene_set_enrichment.html +++ b/reference/gene_set_enrichment.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -176,7 +176,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:31:55.814905 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:10:44.019232 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_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 43846ba4..2f6f26ab 100644 --- a/reference/gene_set_enrichment_plot.html +++ b/reference/gene_set_enrichment_plot.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -178,7 +178,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:31:57.168311 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:10:45.630596 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_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 db6da217..aeb36000 100644 --- a/reference/geom_spatial.html +++ b/reference/geom_spatial.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -175,7 +175,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-05-24 06:31:59.036277 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:10:47.783319 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/get_colors.html b/reference/get_colors.html index 20813d9e..272b883e 100644 --- a/reference/get_colors.html +++ b/reference/get_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -105,7 +105,7 @@

Examples


 ## Obtain the necessary data
 if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
-#> 2024-05-24 06:32:14.236607 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
+#> 2024-05-24 18:11:03.662914 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_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 9157c862..b7f9b6ec 100644
--- a/reference/img_edit.html
+++ b/reference/img_edit.html
@@ -19,7 +19,7 @@
       
       
         spatialLIBD
-        1.17.1
+        1.17.2
@@ -222,7 +222,7 @@

Examples

x <- img_edit(spe, sampleid = "151507", brightness = 25) plot(x) } -#> 2024-05-24 06:32:15.433287 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:11:05.105078 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/img_update.html b/reference/img_update.html index 76c61e13..19a9f0bb 100644 --- a/reference/img_update.html +++ b/reference/img_update.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -139,7 +139,7 @@

Examples

## Reduce brightness to 25% and update the imgData() imgData(img_update(spe, sampleid = "151507", brightness = 25)) } -#> 2024-05-24 06:32:30.927966 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:11:21.079784 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 3c7f7575..c09e2c2e 100644 --- a/reference/img_update_all.html +++ b/reference/img_update_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -138,7 +138,7 @@

Examples

## update the imgData() imgData(img_update_all(spe, brightness = 25)) } -#> 2024-05-24 06:32:44.879917 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:11:35.765711 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 aab1e57f..cc703ceb 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/layer_boxplot.html b/reference/layer_boxplot.html index 0fe510ed..f4125cb2 100644 --- a/reference/layer_boxplot.html +++ b/reference/layer_boxplot.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -185,9 +185,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:33:01.260983 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:11:52.913796 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-24 06:33:02.130377 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:11:54.114222 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_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 05495279..6afefc72 100644 --- a/reference/layer_matrix_plot.html +++ b/reference/layer_matrix_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/layer_stat_cor.html b/reference/layer_stat_cor.html index 2381e54c..0f0a61d6 100644 --- a/reference/layer_stat_cor.html +++ b/reference/layer_stat_cor.html @@ -17,7 +17,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -156,7 +156,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:33:05.460015 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:11:58.058793 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_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 e4172542..aceedb5a 100644 --- a/reference/layer_stat_cor_plot.html +++ b/reference/layer_stat_cor_plot.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -145,7 +145,7 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:33:07.342236 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:12:00.296526 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_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 d0335932..02c4a979 100644 --- a/reference/libd_layer_colors.html +++ b/reference/libd_layer_colors.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/locate_images.html b/reference/locate_images.html index 68d6b254..f8104234 100644 --- a/reference/locate_images.html +++ b/reference/locate_images.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/multi_gene_pca.html b/reference/multi_gene_pca.html index 31989194..076a3f70 100644 --- a/reference/multi_gene_pca.html +++ b/reference/multi_gene_pca.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/multi_gene_sparsity.html b/reference/multi_gene_sparsity.html index e515ed4a..9749384e 100644 --- a/reference/multi_gene_sparsity.html +++ b/reference/multi_gene_sparsity.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/multi_gene_z_score.html b/reference/multi_gene_z_score.html index 57cdd506..2b091342 100644 --- a/reference/multi_gene_z_score.html +++ b/reference/multi_gene_z_score.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/read10xVisiumAnalysis.html b/reference/read10xVisiumAnalysis.html index 9a6b4b30..1c1ed88f 100644 --- a/reference/read10xVisiumAnalysis.html +++ b/reference/read10xVisiumAnalysis.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/read10xVisiumWrapper.html b/reference/read10xVisiumWrapper.html index 4deafd3c..03864d93 100644 --- a/reference/read10xVisiumWrapper.html +++ b/reference/read10xVisiumWrapper.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/registration_block_cor.html b/reference/registration_block_cor.html index 10599ebd..e4b85746 100644 --- a/reference/registration_block_cor.html +++ b/reference/registration_block_cor.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -146,9 +146,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-24 06:33:09.492637 make pseudobulk object -#> 2024-05-24 06:33:09.717641 drop lowly expressed genes -#> 2024-05-24 06:33:09.785735 normalize expression +#> 2024-05-24 18:12:02.458717 make pseudobulk object +#> 2024-05-24 18:12:02.689116 drop lowly expressed genes +#> 2024-05-24 18:12:02.759157 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") -#> 2024-05-24 06:33:09.862063 create model matrix +#> 2024-05-24 18:12:02.834893 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) -#> 2024-05-24 06:33:09.876051 run duplicateCorrelation() -#> 2024-05-24 06:33:11.16522 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 18:12:02.847373 run duplicateCorrelation() +#> 2024-05-24 18:12:04.100302 The estimated correlation is: -0.0187869166526901 diff --git a/reference/registration_model.html b/reference/registration_model.html index 29bebcbc..5165e0d0 100644 --- a/reference/registration_model.html +++ b/reference/registration_model.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -148,9 +148,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-24 06:33:11.596051 make pseudobulk object -#> 2024-05-24 06:33:11.777462 drop lowly expressed genes -#> 2024-05-24 06:33:11.829713 normalize expression +#> 2024-05-24 18:12:04.530455 make pseudobulk object +#> 2024-05-24 18:12:04.712465 drop lowly expressed genes +#> 2024-05-24 18:12:04.766214 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") -#> 2024-05-24 06:33:11.901191 create model matrix +#> 2024-05-24 18:12:04.840138 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 b8311d16..92b5328f 100644 --- a/reference/registration_pseudobulk.html +++ b/reference/registration_pseudobulk.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -159,9 +159,9 @@

Examples

## Pseudo-bulk sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-24 06:33:12.342844 make pseudobulk object -#> 2024-05-24 06:33:12.48958 drop lowly expressed genes -#> 2024-05-24 06:33:12.54108 normalize expression +#> 2024-05-24 18:12:05.294996 make pseudobulk object +#> 2024-05-24 18:12:05.445971 drop lowly expressed genes +#> 2024-05-24 18:12:05.499413 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 20c56458..db7dcb1a 100644 --- a/reference/registration_stats_anova.html +++ b/reference/registration_stats_anova.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -180,9 +180,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-24 06:33:13.153337 make pseudobulk object -#> 2024-05-24 06:33:13.304993 drop lowly expressed genes -#> 2024-05-24 06:33:13.357234 normalize expression +#> 2024-05-24 18:12:06.104832 make pseudobulk object +#> 2024-05-24 18:12:06.257231 drop lowly expressed genes +#> 2024-05-24 18:12:06.310355 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") -#> 2024-05-24 06:33:13.428298 create model matrix +#> 2024-05-24 18:12:06.383227 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) -#> 2024-05-24 06:33:13.438893 run duplicateCorrelation() -#> 2024-05-24 06:33:14.715774 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 18:12:06.394329 run duplicateCorrelation() +#> 2024-05-24 18:12:07.678114 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" ) -#> 2024-05-24 06:33:14.727552 computing F-statistics +#> 2024-05-24 18:12:07.689973 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" ) -#> 2024-05-24 06:33:14.812758 computing F-statistics +#> 2024-05-24 18:12:07.750539 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" ) -#> 2024-05-24 06:33:14.860679 computing F-statistics +#> 2024-05-24 18:12:07.798676 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 9c83db9f..98077572 100644 --- a/reference/registration_stats_enrichment.html +++ b/reference/registration_stats_enrichment.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -171,9 +171,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-24 06:33:15.413919 make pseudobulk object -#> 2024-05-24 06:33:15.560752 drop lowly expressed genes -#> 2024-05-24 06:33:15.612442 normalize expression +#> 2024-05-24 18:12:08.358016 make pseudobulk object +#> 2024-05-24 18:12:08.50857 drop lowly expressed genes +#> 2024-05-24 18:12:08.561794 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") -#> 2024-05-24 06:33:15.685704 create model matrix +#> 2024-05-24 18:12:08.63425 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) -#> 2024-05-24 06:33:15.69641 run duplicateCorrelation() -#> 2024-05-24 06:33:16.977484 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 18:12:08.645086 run duplicateCorrelation() +#> 2024-05-24 18:12:09.935076 The estimated correlation is: -0.0187869166526901 results_enrichment <- registration_stats_enrichment(sce_pseudo, block_cor, "age", gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-05-24 06:33:16.980926 computing enrichment statistics -#> 2024-05-24 06:33:17.093063 extract and reformat enrichment results +#> 2024-05-24 18:12:09.938738 computing enrichment statistics +#> 2024-05-24 18:12:10.051605 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" ) -#> 2024-05-24 06:33:17.12484 computing enrichment statistics -#> 2024-05-24 06:33:17.224913 extract and reformat enrichment results +#> 2024-05-24 18:12:10.083738 computing enrichment statistics +#> 2024-05-24 18:12:10.185475 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 49d84646..343adf1b 100644 --- a/reference/registration_stats_pairwise.html +++ b/reference/registration_stats_pairwise.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -173,9 +173,9 @@

Examples

#> #> rgstr_> ## Pseudo-bulk #> rgstr_> sce_pseudo <- registration_pseudobulk(sce, "Cell_Cycle", "sample_id", c("age"), min_ncells = NULL) -#> 2024-05-24 06:33:17.699434 make pseudobulk object -#> 2024-05-24 06:33:17.847348 drop lowly expressed genes -#> 2024-05-24 06:33:17.899635 normalize expression +#> 2024-05-24 18:12:10.662705 make pseudobulk object +#> 2024-05-24 18:12:10.811846 drop lowly expressed genes +#> 2024-05-24 18:12:10.864563 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") -#> 2024-05-24 06:33:17.970375 create model matrix +#> 2024-05-24 18:12:10.93646 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) -#> 2024-05-24 06:33:17.981199 run duplicateCorrelation() -#> 2024-05-24 06:33:19.275373 The estimated correlation is: -0.0187869166526901 +#> 2024-05-24 18:12:10.947512 run duplicateCorrelation() +#> 2024-05-24 18:12:12.237077 The estimated correlation is: -0.0187869166526901 results_pairwise <- registration_stats_pairwise(sce_pseudo, registration_mod, block_cor, gene_ensembl = "ensembl", gene_name = "gene_name" ) -#> 2024-05-24 06:33:19.277411 running the baseline pairwise model -#> 2024-05-24 06:33:19.29375 computing pairwise statistics +#> 2024-05-24 18:12:12.238947 running the baseline pairwise model +#> 2024-05-24 18:12:12.254946 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" ) -#> 2024-05-24 06:33:19.357572 running the baseline pairwise model -#> 2024-05-24 06:33:19.374381 computing pairwise statistics +#> 2024-05-24 18:12:12.318609 running the baseline pairwise model +#> 2024-05-24 18:12:12.335546 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 7f337310..124729f3 100644 --- a/reference/registration_wrapper.html +++ b/reference/registration_wrapper.html @@ -22,7 +22,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -200,18 +200,18 @@

Examples

sce, "Cell_Cycle", "sample_id", c("age"), "ensembl", "gene_name", "wrapper" ) -#> 2024-05-24 06:33:19.889828 make pseudobulk object -#> 2024-05-24 06:33:20.063577 dropping 9 pseudo-bulked samples that are below 'min_ncells'. -#> 2024-05-24 06:33:20.083559 drop lowly expressed genes -#> 2024-05-24 06:33:20.134552 normalize expression -#> 2024-05-24 06:33:20.189356 create model matrix -#> 2024-05-24 06:33:20.199538 run duplicateCorrelation() -#> 2024-05-24 06:33:22.589525 The estimated correlation is: -0.0783081238514532 -#> 2024-05-24 06:33:22.591635 computing enrichment statistics -#> 2024-05-24 06:33:22.702667 extract and reformat enrichment results -#> 2024-05-24 06:33:22.727031 running the baseline pairwise model -#> 2024-05-24 06:33:22.744089 computing pairwise statistics -#> 2024-05-24 06:33:22.815567 computing F-statistics +#> 2024-05-24 18:12:12.848738 make pseudobulk object +#> 2024-05-24 18:12:13.024713 dropping 9 pseudo-bulked samples that are below 'min_ncells'. +#> 2024-05-24 18:12:13.04496 drop lowly expressed genes +#> 2024-05-24 18:12:13.097269 normalize expression +#> 2024-05-24 18:12:13.15242 create model matrix +#> 2024-05-24 18:12:13.162664 run duplicateCorrelation() +#> 2024-05-24 18:12:15.550921 The estimated correlation is: -0.0783081238514532 +#> 2024-05-24 18:12:15.553011 computing enrichment statistics +#> 2024-05-24 18:12:15.664135 extract and reformat enrichment results +#> 2024-05-24 18:12:15.688548 running the baseline pairwise model +#> 2024-05-24 18:12:15.705656 computing pairwise statistics +#> 2024-05-24 18:12:15.777165 computing F-statistics diff --git a/reference/run_app.html b/reference/run_app.html index cd3e65f1..0b5a564a 100644 --- a/reference/run_app.html +++ b/reference/run_app.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/sce_to_spe.html b/reference/sce_to_spe.html index 59baa144..8f99d56a 100644 --- a/reference/sce_to_spe.html +++ b/reference/sce_to_spe.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -127,7 +127,7 @@

Examples

## Transform it to a SpatialExperiment object spe <- sce_to_spe(sce) } -#> 2024-05-24 06:33:24.996505 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:12:18.219373 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 c3314ce4..db71f72f 100644 --- a/reference/sig_genes_extract.html +++ b/reference/sig_genes_extract.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -156,9 +156,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:33:37.791004 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:12:31.71533 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-24 06:33:38.882315 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:12:32.953542 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_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 6205e7c0..c330570e 100644 --- a/reference/sig_genes_extract_all.html +++ b/reference/sig_genes_extract_all.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -128,9 +128,9 @@

Examples

if (!exists("modeling_results")) { modeling_results <- fetch_data(type = "modeling_results") } -#> 2024-05-24 06:33:42.675083 loading file /github/home/.cache/R/BiocFileCache/2723d218943_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 +#> 2024-05-24 18:12:37.007081 loading file /github/home/.cache/R/BiocFileCache/2e74a1d6212_Human_DLPFC_Visium_modeling_results.Rdata%3Fdl%3D1 if (!exists("sce_layer")) sce_layer <- fetch_data(type = "sce_layer") -#> 2024-05-24 06:33:43.573064 loading file /github/home/.cache/R/BiocFileCache/272335c9fe4_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:12:38.238185 loading file /github/home/.cache/R/BiocFileCache/2e71f430d0f_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 e6595cc1..56b0690b 100644 --- a/reference/sort_clusters.html +++ b/reference/sort_clusters.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/spatialLIBD-package.html b/reference/spatialLIBD-package.html index b99217c1..eda56bb6 100644 --- a/reference/spatialLIBD-package.html +++ b/reference/spatialLIBD-package.html @@ -18,7 +18,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html index e395bddd..560d08d7 100644 --- a/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html +++ b/reference/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 diff --git a/reference/vis_clus.html b/reference/vis_clus.html index a4ff208d..07ef8bb1 100644 --- a/reference/vis_clus.html +++ b/reference/vis_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -232,7 +232,7 @@

Examples

) print(p4) } -#> 2024-05-24 06:33:46.755551 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:12:41.769123 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 07ef5673..ecd87c08 100644 --- a/reference/vis_clus_p.html +++ b/reference/vis_clus_p.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -202,7 +202,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-05-24 06:34:06.16246 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:13:05.295522 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 diff --git a/reference/vis_gene.html b/reference/vis_gene.html index 2310a0ba..85ae3183 100644 --- a/reference/vis_gene.html +++ b/reference/vis_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -331,7 +331,7 @@

Examples

) print(p8) } -#> 2024-05-24 06:34:21.777627 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:13:20.698758 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 0af2eea4..78d9bb47 100644 --- a/reference/vis_gene_p.html +++ b/reference/vis_gene_p.html @@ -21,7 +21,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -220,7 +220,7 @@

Examples

## Clean up rm(spe_sub) } -#> 2024-05-24 06:34:47.45786 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:13:47.16173 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 0fd03440..6faf3ee0 100644 --- a/reference/vis_grid_clus.html +++ b/reference/vis_grid_clus.html @@ -19,7 +19,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -227,7 +227,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-05-24 06:35:02.328426 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:14:02.563202 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_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 ed33831a..5c0b5fb1 100644 --- a/reference/vis_grid_gene.html +++ b/reference/vis_grid_gene.html @@ -20,7 +20,7 @@ spatialLIBD - 1.17.1 + 1.17.2 @@ -246,7 +246,7 @@

Examples

## for subject 3 cowplot::plot_grid(plotlist = p_list, ncol = 2) } -#> 2024-05-24 06:35:18.741817 loading file /github/home/.cache/R/BiocFileCache/d401e78709e_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1 +#> 2024-05-24 18:14:19.335008 loading file /github/home/.cache/R/BiocFileCache/db65995fbcb_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1