diff --git a/404.html b/404.html index 107f980..cc78b33 100644 --- a/404.html +++ b/404.html @@ -33,7 +33,7 @@ iSEEu - 1.15.1 + 1.17.0 @@ -92,7 +92,7 @@

Page not found (404)

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html index cb7b8bc..fcaa02b 100644 --- a/CODE_OF_CONDUCT.html +++ b/CODE_OF_CONDUCT.html @@ -17,7 +17,7 @@ iSEEu - 1.15.1 + 1.17.0 @@ -132,7 +132,7 @@

Attribution -

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/LICENSE-text.html b/LICENSE-text.html index 469a1c6..4ded9f9 100644 --- a/LICENSE-text.html +++ b/LICENSE-text.html @@ -17,7 +17,7 @@ iSEEu - 1.15.1 + 1.17.0 @@ -87,7 +87,7 @@

License

-

Site built with pkgdown 2.0.7.9000.

+

Site built with pkgdown 2.0.9.9000.

diff --git a/articles/iSEEu.html b/articles/iSEEu.html index e2e4aed..db2e816 100644 --- a/articles/iSEEu.html +++ b/articles/iSEEu.html @@ -34,7 +34,7 @@ iSEEu - 1.15.1 + 1.17.0 @@ -97,7 +97,7 @@

Aaron infinite.monkeys.with.keyboards@gmail.com -

27 March 2024

+

2 May 2024

Source: vignettes/iSEEu.Rmd @@ -518,7 +518,7 @@

Session information
 sessionInfo()
-
## R Under development (unstable) (2024-03-24 r86185)
+
## R version 4.4.0 Patched (2024-04-24 r86483)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -542,98 +542,98 @@ 
Session information## [8] base     
 ## 
 ## other attached packages:
-##  [1] scater_1.31.2               ggplot2_3.5.0              
-##  [3] scuttle_1.13.1              scRNAseq_2.17.7            
-##  [5] edgeR_4.1.19                limma_3.59.6               
-##  [7] airway_1.23.0               iSEEu_1.15.1               
-##  [9] iSEEhex_1.5.0               iSEE_2.15.0                
-## [11] SingleCellExperiment_1.25.0 SummarizedExperiment_1.33.3
-## [13] Biobase_2.63.0              GenomicRanges_1.55.4       
-## [15] GenomeInfoDb_1.39.9         IRanges_2.37.1             
-## [17] S4Vectors_0.41.5            BiocGenerics_0.49.1        
-## [19] MatrixGenerics_1.15.0       matrixStats_1.2.0          
-## [21] BiocStyle_2.31.0           
+##  [1] scater_1.32.0               ggplot2_3.5.1              
+##  [3] scuttle_1.14.0              scRNAseq_2.17.9            
+##  [5] edgeR_4.2.0                 limma_3.60.0               
+##  [7] airway_1.23.0               iSEEu_1.17.0               
+##  [9] iSEEhex_1.5.0               iSEE_2.15.1                
+## [11] SingleCellExperiment_1.26.0 SummarizedExperiment_1.33.3
+## [13] Biobase_2.64.0              GenomicRanges_1.55.4       
+## [15] GenomeInfoDb_1.40.0         IRanges_2.38.0             
+## [17] S4Vectors_0.42.0            BiocGenerics_0.50.0        
+## [19] MatrixGenerics_1.16.0       matrixStats_1.3.0          
+## [21] BiocStyle_2.32.0           
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] splines_4.4.0             later_1.3.2              
-##   [3] aws.s3_0.3.21             BiocIO_1.13.0            
-##   [5] bitops_1.0-7              filelock_1.0.3           
-##   [7] tibble_3.2.1              XML_3.99-0.16.1          
-##   [9] lifecycle_1.0.4           httr2_1.0.0              
-##  [11] doParallel_1.0.17         lattice_0.22-6           
-##  [13] ensembldb_2.27.1          alabaster.base_1.3.23    
-##  [15] magrittr_2.0.3            sass_0.4.9               
-##  [17] rmarkdown_2.26            jquerylib_0.1.4          
-##  [19] yaml_2.3.8                httpuv_1.6.15            
-##  [21] DBI_1.2.2                 RColorBrewer_1.1-3       
-##  [23] abind_1.4-5               zlibbioc_1.49.3          
-##  [25] Rtsne_0.17                purrr_1.0.2              
-##  [27] AnnotationFilter_1.27.0   RCurl_1.98-1.14          
-##  [29] rappdirs_0.3.3            circlize_0.4.16          
-##  [31] GenomeInfoDbData_1.2.11   ggrepel_0.9.5            
-##  [33] irlba_2.3.5.1             alabaster.sce_1.3.3      
-##  [35] DelayedMatrixStats_1.25.1 pkgdown_2.0.7.9000       
-##  [37] codetools_0.2-19          DelayedArray_0.29.9      
-##  [39] DT_0.32                   xml2_1.3.6               
-##  [41] tidyselect_1.2.1          shape_1.4.6.1            
-##  [43] viridis_0.6.5             ScaledMatrix_1.11.1      
-##  [45] shinyWidgets_0.8.3        BiocFileCache_2.11.1     
-##  [47] base64enc_0.1-3           GenomicAlignments_1.39.4 
-##  [49] jsonlite_1.8.8            BiocNeighbors_1.21.2     
-##  [51] GetoptLong_1.0.5          iterators_1.0.14         
-##  [53] systemfonts_1.0.6         foreach_1.5.2            
-##  [55] tools_4.4.0               ragg_1.3.0               
-##  [57] Rcpp_1.0.12               glue_1.7.0               
-##  [59] gridExtra_2.3             SparseArray_1.3.4        
-##  [61] xfun_0.43                 mgcv_1.9-1               
-##  [63] dplyr_1.1.4               HDF5Array_1.31.6         
-##  [65] gypsum_0.99.15            withr_3.0.0              
-##  [67] shinydashboard_0.7.2      BiocManager_1.30.22      
-##  [69] fastmap_1.1.1             rhdf5filters_1.15.4      
-##  [71] fansi_1.0.6               shinyjs_2.1.0            
-##  [73] rsvd_1.0.5                digest_0.6.35            
-##  [75] R6_2.5.1                  mime_0.12                
-##  [77] textshaping_0.3.7         colorspace_2.1-0         
-##  [79] RSQLite_2.3.5             utf8_1.2.4               
+##   [3] BiocIO_1.14.0             bitops_1.0-7             
+##   [5] filelock_1.0.3            tibble_3.2.1             
+##   [7] XML_3.99-0.16.1           lifecycle_1.0.4          
+##   [9] httr2_1.0.1               doParallel_1.0.17        
+##  [11] lattice_0.22-6            ensembldb_2.28.0         
+##  [13] alabaster.base_1.4.0      magrittr_2.0.3           
+##  [15] sass_0.4.9                rmarkdown_2.26.2         
+##  [17] jquerylib_0.1.4           yaml_2.3.8               
+##  [19] httpuv_1.6.15             DBI_1.2.2                
+##  [21] RColorBrewer_1.1-3        abind_1.4-5              
+##  [23] zlibbioc_1.50.0           Rtsne_0.17               
+##  [25] purrr_1.0.2               AnnotationFilter_1.28.0  
+##  [27] RCurl_1.98-1.14           rappdirs_0.3.3           
+##  [29] circlize_0.4.16           GenomeInfoDbData_1.2.12  
+##  [31] ggrepel_0.9.5             irlba_2.3.5.1            
+##  [33] alabaster.sce_1.4.0       DelayedMatrixStats_1.26.0
+##  [35] pkgdown_2.0.9.9000        codetools_0.2-20         
+##  [37] DelayedArray_0.30.0       DT_0.33                  
+##  [39] tidyselect_1.2.1          shape_1.4.6.1            
+##  [41] UCSC.utils_1.0.0          viridis_0.6.5            
+##  [43] ScaledMatrix_1.12.0       shinyWidgets_0.8.6       
+##  [45] BiocFileCache_2.12.0      GenomicAlignments_1.40.0 
+##  [47] jsonlite_1.8.8            BiocNeighbors_1.22.0     
+##  [49] GetoptLong_1.0.5          iterators_1.0.14         
+##  [51] systemfonts_1.0.6         foreach_1.5.2            
+##  [53] tools_4.4.0               ragg_1.3.0               
+##  [55] Rcpp_1.0.12               glue_1.7.0               
+##  [57] gridExtra_2.3             SparseArray_1.4.0        
+##  [59] xfun_0.43                 mgcv_1.9-1               
+##  [61] dplyr_1.1.4               HDF5Array_1.32.0         
+##  [63] gypsum_1.0.0              withr_3.0.0              
+##  [65] shinydashboard_0.7.2      BiocManager_1.30.22      
+##  [67] fastmap_1.1.1             rhdf5filters_1.16.0      
+##  [69] fansi_1.0.6               shinyjs_2.1.0            
+##  [71] rsvd_1.0.5                digest_0.6.35            
+##  [73] R6_2.5.1                  mime_0.12                
+##  [75] textshaping_0.3.7         colorspace_2.1-0         
+##  [77] listviewer_4.0.0          RSQLite_2.3.6            
+##  [79] paws.storage_0.5.0        utf8_1.2.4               
 ##  [81] generics_0.1.3            hexbin_1.28.3            
-##  [83] rtracklayer_1.63.1        httr_1.4.7               
-##  [85] htmlwidgets_1.6.4         S4Arrays_1.3.6           
-##  [87] pkgconfig_2.0.3           gtable_0.3.4             
-##  [89] blob_1.2.4                ComplexHeatmap_2.19.0    
-##  [91] XVector_0.43.1            htmltools_0.5.8          
-##  [93] bookdown_0.38             ProtGenerics_1.35.4      
+##  [83] rtracklayer_1.64.0        httr_1.4.7               
+##  [85] htmlwidgets_1.6.4         S4Arrays_1.4.0           
+##  [87] pkgconfig_2.0.3           gtable_0.3.5             
+##  [89] blob_1.2.4                ComplexHeatmap_2.20.0    
+##  [91] XVector_0.44.0            htmltools_0.5.8.1        
+##  [93] bookdown_0.39             ProtGenerics_1.36.0      
 ##  [95] rintrojs_0.3.4            clue_0.3-65              
-##  [97] scales_1.3.0              alabaster.matrix_1.3.13  
-##  [99] png_0.1-8                 knitr_1.45               
+##  [97] scales_1.3.0              alabaster.matrix_1.4.0   
+##  [99] png_0.1-8                 knitr_1.46               
 ## [101] rjson_0.2.21              nlme_3.1-164             
 ## [103] curl_5.2.1                shinyAce_0.4.2           
-## [105] cachem_1.0.8              rhdf5_2.47.6             
+## [105] cachem_1.0.8              rhdf5_2.48.0             
 ## [107] GlobalOptions_0.1.2       BiocVersion_3.19.1       
 ## [109] parallel_4.4.0            miniUI_0.1.1.1           
 ## [111] vipor_0.4.7               AnnotationDbi_1.65.2     
 ## [113] restfulr_0.0.15           desc_1.4.3               
 ## [115] pillar_1.9.0              grid_4.4.0               
-## [117] alabaster.schemas_1.3.1   vctrs_0.6.5              
-## [119] promises_1.2.1            BiocSingular_1.19.0      
-## [121] beachmat_2.19.2           dbplyr_2.5.0             
+## [117] alabaster.schemas_1.4.0   vctrs_0.6.5              
+## [119] promises_1.3.0            BiocSingular_1.20.0      
+## [121] beachmat_2.20.0           dbplyr_2.5.0             
 ## [123] xtable_1.8-4              cluster_2.1.6            
 ## [125] beeswarm_0.4.0            evaluate_0.23            
-## [127] GenomicFeatures_1.55.4    cli_3.6.2                
+## [127] GenomicFeatures_1.56.0    cli_3.6.2                
 ## [129] locfit_1.5-9.9            compiler_4.4.0           
-## [131] Rsamtools_2.19.4          rlang_1.1.3              
-## [133] crayon_1.5.2              aws.signature_0.6.0      
-## [135] ggbeeswarm_0.7.2          fs_1.6.3                 
-## [137] viridisLite_0.4.2         alabaster.se_1.3.4       
-## [139] BiocParallel_1.37.1       munsell_0.5.0            
-## [141] Biostrings_2.71.5         lazyeval_0.2.2           
+## [131] Rsamtools_2.20.0          rlang_1.1.3              
+## [133] crayon_1.5.2              paws.common_0.7.2        
+## [135] ggbeeswarm_0.7.2          fs_1.6.4                 
+## [137] viridisLite_0.4.2         alabaster.se_1.4.0       
+## [139] BiocParallel_1.38.0       munsell_0.5.1            
+## [141] Biostrings_2.72.0         lazyeval_0.2.2           
 ## [143] colourpicker_1.3.0        Matrix_1.7-0             
-## [145] ExperimentHub_2.11.1      sparseMatrixStats_1.15.0 
-## [147] bit64_4.0.5               Rhdf5lib_1.25.1          
-## [149] KEGGREST_1.43.0           statmod_1.5.0            
-## [151] shiny_1.8.1               alabaster.ranges_1.3.3   
-## [153] highr_0.10                AnnotationHub_3.11.3     
+## [145] ExperimentHub_2.12.0      sparseMatrixStats_1.16.0 
+## [147] bit64_4.0.5               Rhdf5lib_1.26.0          
+## [149] KEGGREST_1.44.0           statmod_1.5.0            
+## [151] shiny_1.8.1.1             alabaster.ranges_1.4.0   
+## [153] highr_0.10                AnnotationHub_3.12.0     
 ## [155] fontawesome_0.5.2         igraph_2.0.3             
-## [157] memoise_2.0.1             bslib_0.6.2              
+## [157] memoise_2.0.1             bslib_0.7.0              
 ## [159] bit_4.0.5

 
 

@@ -666,7 +666,7 @@ 
References
   

-
Site built with pkgdown 2.0.7.9000.

+
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/articles/index.html b/articles/index.html
index 014a24c..7a59a5d 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -65,7 +65,7 @@ 
All vignettes

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/authors.html b/authors.html
index 9d91607..b08b3fd 100644
--- a/authors.html
+++ b/authors.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -82,13 +82,13 @@ 
Citation

 
     
Rue-Albrecht K, Soneson C, Marini F, Lun A (2024).
 iSEEu: iSEE Universe.
-R package version 1.15.1, https://github.com/iSEE/iSEEu. 
+R package version 1.17.0, https://github.com/iSEE/iSEEu. 
 

     
@Manual{,
   title = {iSEEu: iSEE Universe},
   author = {Kevin Rue-Albrecht and Charlotte Soneson and Federico Marini and Aaron Lun},
   year = {2024},
-  note = {R package version 1.15.1},
+  note = {R package version 1.17.0},
   url = {https://github.com/iSEE/iSEEu},
 }

 
@@ -103,7 +103,7 @@ 
Citation

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/index.html b/index.html
index fa167d2..16180fe 100644
--- a/index.html
+++ b/index.html
@@ -34,7 +34,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -234,7 +234,7 @@ 
Dev status

 
 

   

-
Site built with pkgdown 2.0.7.9000.

+
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/news/index.html b/news/index.html
index 0f05e90..3058292 100644
--- a/news/index.html
+++ b/news/index.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -216,7 +216,7 @@ 
iSEEu 0.1.0
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/pkgdown.yml b/pkgdown.yml
index c29091e..717fc1f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,7 +1,7 @@
 pandoc: 3.1.1
-pkgdown: 2.0.7.9000
-pkgdown_sha: 676cf1dce39e4dc5aa1bcb671b1e14e992589a0a
+pkgdown: 2.0.9.9000
+pkgdown_sha: 9a6bbfc6ecf3aaf94406783beb0154fec0f3e87c
 articles:
   iSEEu: iSEEu.html
-last_built: 2024-03-27T14:04Z
+last_built: 2024-05-02T16:21Z
 
diff --git a/reference/AggregatedDotPlot.html b/reference/AggregatedDotPlot.html
index 810d583..d01d88b 100644
--- a/reference/AggregatedDotPlot.html
+++ b/reference/AggregatedDotPlot.html
@@ -19,7 +19,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -182,7 +182,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/DynamicMarkerTable-class.html b/reference/DynamicMarkerTable-class.html
index 3cb8567..42c29de 100644
--- a/reference/DynamicMarkerTable-class.html
+++ b/reference/DynamicMarkerTable-class.html
@@ -20,7 +20,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -143,7 +143,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/DynamicReducedDimensionPlot-class.html b/reference/DynamicReducedDimensionPlot-class.html
index b9b6ef9..d798bda 100644
--- a/reference/DynamicReducedDimensionPlot-class.html
+++ b/reference/DynamicReducedDimensionPlot-class.html
@@ -19,7 +19,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -139,7 +139,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/FeatureSetTable-class.html b/reference/FeatureSetTable-class.html
index 99c41a9..1a16334 100644
--- a/reference/FeatureSetTable-class.html
+++ b/reference/FeatureSetTable-class.html
@@ -20,7 +20,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -163,7 +163,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/GeneSetTable-class.html b/reference/GeneSetTable-class.html
index 74a9a06..a2bd837 100644
--- a/reference/GeneSetTable-class.html
+++ b/reference/GeneSetTable-class.html
@@ -18,7 +18,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -161,7 +161,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/LogFCLogFCPlot-class.html b/reference/LogFCLogFCPlot-class.html
index e7cadd1..b861fc8 100644
--- a/reference/LogFCLogFCPlot-class.html
+++ b/reference/LogFCLogFCPlot-class.html
@@ -18,7 +18,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -155,7 +155,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/MAPlot-class.html b/reference/MAPlot-class.html
index b8280d9..59b5504 100644
--- a/reference/MAPlot-class.html
+++ b/reference/MAPlot-class.html
@@ -18,7 +18,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -151,7 +151,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/MarkdownBoard-class.html b/reference/MarkdownBoard-class.html
index 3e38660..76ab874 100644
--- a/reference/MarkdownBoard-class.html
+++ b/reference/MarkdownBoard-class.html
@@ -18,7 +18,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -123,7 +123,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/VolcanoPlot-class.html b/reference/VolcanoPlot-class.html
index e433f79..f93d059 100644
--- a/reference/VolcanoPlot-class.html
+++ b/reference/VolcanoPlot-class.html
@@ -18,7 +18,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -150,7 +150,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/createGeneSetCommands.html b/reference/createGeneSetCommands.html
index 9fff024..2b47ffb 100644
--- a/reference/createGeneSetCommands.html
+++ b/reference/createGeneSetCommands.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -65,15 +65,15 @@ 
Create gene set commands

 
     

     
Arguments

-    
collections

+    
collections

 
Character vectors specifying the gene set collections of interest.

 
 
-
organism

+
organism

 
String containing the org.*.eg.db package to use to extract mappings of gene sets to gene IDs.

 
 
-
identifier

+
identifier

 
String specifying the identifier to use to extract IDs for the organism package.

 
 

@@ -132,7 +132,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/defunct.html b/reference/defunct.html
index 58690ad..d3e61b9 100644
--- a/reference/defunct.html
+++ b/reference/defunct.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -71,7 +71,7 @@ 
Defunct functions

 
     

     
Arguments

-    
...

+    
...

 
Ignored.

 
 

@@ -98,7 +98,7 @@ 
Author

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/global-FeatureSetCommands.html b/reference/global-FeatureSetCommands.html
index 2c28012..a74a224 100644
--- a/reference/global-FeatureSetCommands.html
+++ b/reference/global-FeatureSetCommands.html
@@ -18,7 +18,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -63,7 +63,7 @@ 
Global feature set commands

 
     

     
Arguments

-    
value

+    
value

 
A list of two character vectors named "collections" and "sets".
 Both vectors should be of the same length and have the same names.
 Vectors should contain R commands to create collections and retrieve sets;
@@ -122,7 +122,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/global-TableExtraFields.html b/reference/global-TableExtraFields.html
index 235a5df..361e2f8 100644
--- a/reference/global-TableExtraFields.html
+++ b/reference/global-TableExtraFields.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -63,7 +63,7 @@ 
Global extra table fields

 
     

     
Arguments

-    
value

+    
value

 
A character vector containing the names of extra fields to include.

 
 

@@ -111,7 +111,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/globals-PValuePattern.html b/reference/globals-PValuePattern.html
index 00c500c..a3551a5 100644
--- a/reference/globals-PValuePattern.html
+++ b/reference/globals-PValuePattern.html
@@ -18,7 +18,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -73,7 +73,7 @@ 
Global DE prefixes

 
     

     
Arguments

-    
value

+    
value

 
A character vector containing the acceptable prefixes for each statistic.

 
 

@@ -143,7 +143,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/iSEEu-pkg.html b/reference/iSEEu-pkg.html
index 3396382..2669e07 100644
--- a/reference/iSEEu-pkg.html
+++ b/reference/iSEEu-pkg.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -82,7 +82,7 @@ 
Author

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/index.html b/reference/index.html
index 8a1646c..5fceb34 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -146,7 +146,7 @@ 
All functions 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/modeEmpty.html b/reference/modeEmpty.html
index feb460f..2cdf300 100644
--- a/reference/modeEmpty.html
+++ b/reference/modeEmpty.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -61,7 +61,7 @@ 
App pre-configured to launch with no visible panel

 
     

     
Arguments

-    
...

+    
...

 
Arguments passed to iSEE().

 
 

@@ -145,7 +145,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/modeGating.html b/reference/modeGating.html
index cd4dc55..1643f29 100644
--- a/reference/modeGating.html
+++ b/reference/modeGating.html
@@ -20,7 +20,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -67,27 +67,27 @@ 
App pre-configured to link multiple feature assay plots

 
     

     
Arguments

-    
se

+    
se

 
An object that coercible to
 SingleCellExperiment-class

 
 
-
features

+
features

 
data.frame with columns named x and y
 that define the features on the axes of the linked plots.
 Plots are serially linked from the first row to the last.

 
 
-
plotAssay

+
plotAssay

 
The assay (one of assayNames(se)) to use for the plots
 (character vector of length either 1 or equal to nrow(features)).

 
 
-
...

+
...

 
Additional arguments passed to iSEE().

 
 
-
plotWidth

+
plotWidth

 
The grid width of linked plots (numeric vector of
 length either 1 or equal to nrow(features)

 
@@ -147,7 +147,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/modeReducedDim.html b/reference/modeReducedDim.html
index b548190..8a49e89 100644
--- a/reference/modeReducedDim.html
+++ b/reference/modeReducedDim.html
@@ -19,7 +19,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -71,17 +71,17 @@ 
App pre-configured to compare multiple reduced dimension plots

 
     

     
Arguments

-    
se

+    
se

 
An object that coercible to SingleCellExperiment

 
 
-
includeNames

+
includeNames

 
Character vector with the names of reduced dimensions
 to display as individual panels. The default uses all available in
 reducedDimNames(se).

 
 
-
colorBy

+
colorBy

 
Character scalar controlling coloring of cells. Must match either
 to one of colnames(colData(se)) or rownames(se). If coloring
 by a colData column, a column data plot is opened in addition to the
@@ -90,11 +90,11 @@ 
Arguments

 latter are receiving the color.

 
 
-
...

+
...

 
Additional arguments passed to iSEE.

 
 
-
plotWidth

+
plotWidth

 
The grid width of linked plots (numeric vector of length
 either 1 or equal to length(includeNames)). The total width of
 the window is 12, so plotWidth = 4 for example will show three
@@ -153,7 +153,7 @@ 
Examples

 

 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/registerDEFields.html b/reference/registerDEFields.html
index a79316a..b9193ea 100644
--- a/reference/registerDEFields.html
+++ b/reference/registerDEFields.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -83,23 +83,23 @@ 
Register DE-related fields

 
     

     
Arguments

-    
se

+    
se

 
A SummarizedExperiment to be visualized with various DE-related Panels.
 This is expected to have a number of DE-related fields in its rowData.

 
 
-
fields

+
fields

 
A character vector containing the names of the relevant fields containing the DE statistics.
 Alternatively NULL to remove any existing setting.

 
 
-
patterns

+
patterns

 
A character vector containing partial names,
 to match against the colnames of the rowData to identify relevant fields containing DE statistics.
 Alternatively NULL to remove any existing setting.

 
 
-
defaults

+
defaults

 
Character vector specifying the default patterns to provide when no patterns were registered in se.

 
 

@@ -171,7 +171,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/registerFeatureSetCollections.html b/reference/registerFeatureSetCollections.html
index 717ac25..d16ad27 100644
--- a/reference/registerFeatureSetCollections.html
+++ b/reference/registerFeatureSetCollections.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -67,16 +67,16 @@ 
Register feature set collections

 
     

     
Arguments

-    
se

+    
se

 
The SummarizedExperiment object to be used in iSEE.

 
 
-
collections

+
collections

 
A named list containing one or more CharacterList objects.
 Each entry represents a collection of feature sets (see Details) and should be named.

 
 
-
commands

+
commands

 
A named list containing two character vectors of commands to use to generate collections and sets.

 
 

@@ -160,7 +160,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.

 

 
       
diff --git a/reference/utils-geneset.html b/reference/utils-geneset.html
index 22271e8..ca1bb19 100644
--- a/reference/utils-geneset.html
+++ b/reference/utils-geneset.html
@@ -17,7 +17,7 @@
       
       
         iSEEu
-        1.15.1
+        1.17.0
       
     
 
@@ -71,17 +71,17 @@ 
Gene set utilities

 
     

     
Arguments

-    
value

+    
value

 
For .setIdentifierType and .setOrganism,
 a string containing the type of identifier or organism package to use.

 
For .setGeneSetCommands, a named list containing two character vectors, see Details.

 
 
-
collection

+
collection

 
String specifying the gene set collection.

 
 
-
mode

+
mode

 
String specifying the mode of operation for the returned commands.

 
 

@@ -207,7 +207,7 @@ 
Examples

 
 
 

-  
Site built with pkgdown 2.0.7.9000.

+  
Site built with pkgdown 2.0.9.9000.