diff --git a/articles/WIP/adding-new-methods-to-sparrow.html b/articles/WIP/adding-new-methods-to-sparrow.html index 0c738d0e..f820d41c 100644 --- a/articles/WIP/adding-new-methods-to-sparrow.html +++ b/articles/WIP/adding-new-methods-to-sparrow.html @@ -85,7 +85,7 @@

Adding new methods to sparrow

Steve Lianoglou

-

19 January 2025

+

20 January 2025

Source: vignettes/WIP/adding-new-methods-to-sparrow.Rmd @@ -183,7 +183,7 @@

Reproducibility
 sessionInfo()
-
## R Under development (unstable) (2025-01-08 r87545)
+
## R Under development (unstable) (2025-01-11 r87563)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 24.04.1 LTS
 ## 
@@ -214,10 +214,10 @@ 
Reproducibility##  [7] cachem_1.1.0        knitr_1.49          htmltools_0.5.8.1  
 ## [10] rmarkdown_2.29      lifecycle_1.0.4     cli_3.6.3          
 ## [13] sass_0.4.9          pkgdown_2.1.1       textshaping_0.4.1  
-## [16] jquerylib_0.1.4     systemfonts_1.1.0   compiler_4.5.0     
+## [16] jquerylib_0.1.4     systemfonts_1.2.0   compiler_4.5.0     
 ## [19] tools_4.5.0         ragg_1.3.3          evaluate_1.0.3     
 ## [22] bslib_0.8.0         yaml_2.3.10         BiocManager_1.30.25
-## [25] jsonlite_1.8.9      rlang_1.1.4         fs_1.6.5           
+## [25] jsonlite_1.8.9      rlang_1.1.5         fs_1.6.5           
 ## [28] htmlwidgets_1.6.4

 
 
diff --git a/articles/sparrow.html b/articles/sparrow.html
index 51ae9236..da1318ef 100644
--- a/articles/sparrow.html
+++ b/articles/sparrow.html
@@ -86,7 +86,7 @@ 
Performing gene set enrichment analyses with
                         
Steve
 Lianoglou

             
-            
19 January 2025

+            
20 January 2025

       
       Source: vignettes/sparrow.Rmd
       
@@ -1063,7 +1063,7 @@ 
Reproducibility
-
## R Under development (unstable) (2025-01-08 r87545)
+
## R Under development (unstable) (2025-01-11 r87563)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 24.04.1 LTS
 ## 
@@ -1101,7 +1101,7 @@ 
Reproducibility##  [11] ragg_1.3.3                  vctrs_0.6.5                
 ##  [13] memoise_2.0.1               DelayedMatrixStats_1.29.1  
 ##  [15] htmltools_0.5.8.1           S4Arrays_1.7.1             
-##  [17] Rhdf5lib_1.29.0             SparseArray_1.7.2          
+##  [17] Rhdf5lib_1.29.0             SparseArray_1.7.4          
 ##  [19] rhdf5_2.51.2                sass_0.4.9                 
 ##  [21] bslib_0.8.0                 htmlwidgets_1.6.4          
 ##  [23] desc_1.4.3                  plyr_1.8.9                 
@@ -1117,11 +1117,11 @@ 
Reproducibility##  [43] GenomicRanges_1.59.1        RSQLite_2.3.9              
 ##  [45] beachmat_2.23.6             labeling_0.4.3             
 ##  [47] httr_1.4.7                  abind_1.4-8                
-##  [49] compiler_4.5.0              bit64_4.5.2                
+##  [49] compiler_4.5.0              bit64_4.6.0-1              
 ##  [51] withr_3.0.2                 doParallel_1.0.17          
 ##  [53] backports_1.5.0             BiocParallel_1.41.0        
 ##  [55] viridis_0.6.5               DBI_1.2.3                  
-##  [57] BiasedUrn_2.0.12            HDF5Array_1.35.2           
+##  [57] BiasedUrn_2.0.12            HDF5Array_1.35.6           
 ##  [59] DelayedArray_0.33.3         rjson_0.2.23               
 ##  [61] tools_4.5.0                 msigdbr_7.5.1              
 ##  [63] glue_1.8.0                  rhdf5filters_1.19.0        
@@ -1131,7 +1131,7 @@ 
Reproducibility##  [71] ScaledMatrix_1.15.0         XVector_0.47.2             
 ##  [73] BiocGenerics_0.53.3         foreach_1.5.2              
 ##  [75] pillar_1.10.1               babelgene_22.9             
-##  [77] GSVA_2.1.4                  lattice_0.22-6             
+##  [77] GSVA_2.1.5                  lattice_0.22-6             
 ##  [79] bit_4.5.0.1                 annotate_1.85.0            
 ##  [81] tidyselect_1.2.1            SingleCellExperiment_1.29.1
 ##  [83] locfit_1.5-9.10             Biostrings_2.75.3          
@@ -1140,12 +1140,12 @@ 
Reproducibility##  [89] SummarizedExperiment_1.37.0 stats4_4.5.0               
 ##  [91] xfun_0.50                   Biobase_2.67.0             
 ##  [93] statmod_1.5.0               matrixStats_1.5.0          
-##  [95] UCSC.utils_1.3.0            lazyeval_0.2.2             
+##  [95] UCSC.utils_1.3.1            lazyeval_0.2.2             
 ##  [97] yaml_2.3.10                 evaluate_1.0.3             
 ##  [99] codetools_0.2-20            tibble_3.2.1               
 ## [101] BiocManager_1.30.25         graph_1.85.1               
 ## [103] cli_3.6.3                   ontologyIndex_2.12         
-## [105] xtable_1.8-4                systemfonts_1.1.0          
+## [105] xtable_1.8-4                systemfonts_1.2.0          
 ## [107] munsell_0.5.1               jquerylib_0.1.4            
 ## [109] Rcpp_1.0.14                 GenomeInfoDb_1.43.2        
 ## [111] png_0.1-8                   XML_3.99-0.18              
@@ -1154,7 +1154,7 @@ 
Reproducibility## [117] SpatialExperiment_1.17.0    viridisLite_0.4.2          
 ## [119] GSEABase_1.69.0             scales_1.3.0               
 ## [121] purrr_1.0.2                 crayon_1.5.3               
-## [123] GetoptLong_1.0.5            rlang_1.1.4                
+## [123] GetoptLong_1.0.5            rlang_1.1.5                
 ## [125] KEGGREST_1.47.0

 
 
diff --git a/pkgdown.yml b/pkgdown.yml
index d8b7ad7e..279b5e5c 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,7 +1,7 @@
-pandoc: 3.6.1
+pandoc: 3.6.2
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   WIP/adding-new-methods-to-sparrow: WIP/adding-new-methods-to-sparrow.html
   sparrow: sparrow.html
-last_built: 2025-01-19T11:05Z
+last_built: 2025-01-20T11:06Z
diff --git a/reference/geneSetCollectionURLfunction.html b/reference/geneSetCollectionURLfunction.html
index 6559a417..b29fa9cd 100644
--- a/reference/geneSetCollectionURLfunction.html
+++ b/reference/geneSetCollectionURLfunction.html
@@ -129,7 +129,7 @@ 
Examples

 #>     url <- "http://www.broadinstitute.org/gsea/msigdb/cards/%s.html"
 #>     sprintf(url, name)
 #> }
-#> <bytecode: 0x564712d4ee58>
+#> <bytecode: 0x5571a65062f8>
 #> <environment: namespace:sparrow>
 

     
diff --git a/reference/iplot.html b/reference/iplot.html
index 54c0092f..a2080d46 100644
--- a/reference/iplot.html
+++ b/reference/iplot.html
@@ -179,16 +179,16 @@ 
Examples

       value = c("t-statistic" = "t"),
       type = "density")
 

-iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
+iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
       value = c("log2FC" = "logFC"),
       type = "boxplot")
 

-iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
+iplot(mgr, "BURTON_ADIPOGENESIS_PEAK_AT_2HR",
       value = c("-statistic" = "t"),
       type = "gsea")
 #> Loading required namespace: fgsea
 

-
+