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Author: lazappi

articles/anndataR.html

@@ -446,32 +446,32 @@ sessionInfo()
 #>  [1] anndataR_1.1.2              SingleCellExperiment_1.32.0
 #>  [3] SummarizedExperiment_1.40.0 Biobase_2.70.0             
 #>  [5] GenomicRanges_1.62.1        Seqinfo_1.0.0              
-#>  [7] IRanges_2.44.0              S4Vectors_0.48.0           
+#>  [7] IRanges_2.44.0              S4Vectors_0.48.1           
 #>  [9] BiocGenerics_0.56.0         generics_0.1.4             
 #> [11] MatrixGenerics_1.22.0       matrixStats_1.5.0          
 #> [13] SeuratObject_5.3.0          sp_2.2-1                   
 #> [15] BiocStyle_2.38.0           
 #> 
 #> loaded via a namespace (and not attached):
-#>   [1] RColorBrewer_1.1-3     jsonlite_2.0.0         magrittr_2.0.4        
+#>   [1] RColorBrewer_1.1-3     jsonlite_2.0.0         magrittr_2.0.5        
 #>   [4] spatstat.utils_3.2-2   farver_2.1.2           rmarkdown_2.31        
 #>   [7] fs_2.0.1               ragg_1.5.2             vctrs_0.7.2           
 #>  [10] ROCR_1.0-12            spatstat.explore_3.8-0 htmltools_0.5.9       
-#>  [13] S4Arrays_1.10.1        Rhdf5lib_1.32.0        SparseArray_1.10.9    
+#>  [13] S4Arrays_1.10.1        Rhdf5lib_1.32.0        SparseArray_1.10.10   
 #>  [16] rhdf5_2.54.1           sass_0.4.10            sctransform_0.4.3     
 #>  [19] parallelly_1.46.1      KernSmooth_2.23-26     bslib_0.10.0          
 #>  [22] htmlwidgets_1.6.4      desc_1.4.3             ica_1.0-3             
 #>  [25] plyr_1.8.9             plotly_4.12.0          zoo_1.8-15            
-#>  [28] cachem_1.1.0           igraph_2.2.2           mime_0.13             
+#>  [28] cachem_1.1.0           igraph_2.2.3           mime_0.13             
 #>  [31] lifecycle_1.0.5        pkgconfig_2.0.3        Matrix_1.7-4          
 #>  [34] R6_2.6.1               fastmap_1.2.0          fitdistrplus_1.2-6    
 #>  [37] future_1.70.0          shiny_1.13.0           digest_0.6.39         
 #>  [40] patchwork_1.3.2        tensor_1.5.1           Seurat_5.4.0          
 #>  [43] RSpectra_0.16-2        irlba_2.3.7            textshaping_1.0.5     
-#>  [46] progressr_0.18.0       spatstat.sparse_3.1-0  polyclip_1.10-7       
+#>  [46] progressr_0.19.0       spatstat.sparse_3.1-0  polyclip_1.10-7       
 #>  [49] httr_1.4.8             abind_1.4-8            compiler_4.5.3        
 #>  [52] S7_0.2.1               fastDummies_1.7.5      MASS_7.3-65           
-#>  [55] DelayedArray_0.36.0    tools_4.5.3            lmtest_0.9-40         
+#>  [55] DelayedArray_0.36.1    tools_4.5.3            lmtest_0.9-40         
 #>  [58] otel_0.2.0             httpuv_1.6.17          future.apply_1.20.2   
 #>  [61] goftest_1.2-3          glue_1.8.0             nlme_3.1-168          
 #>  [64] rhdf5filters_1.22.0    promises_1.5.0         grid_4.5.3            
@@ -481,18 +481,18 @@ sessionInfo()
 #>  [76] RcppAnnoy_0.0.23       ggrepel_0.9.8          RANN_2.6.2            
 #>  [79] pillar_1.11.1          stringr_1.6.0          spam_2.11-3           
 #>  [82] RcppHNSW_0.6.0         later_1.4.8            splines_4.5.3         
-#>  [85] dplyr_1.2.0            lattice_0.22-9         deldir_2.0-4          
+#>  [85] dplyr_1.2.1            lattice_0.22-9         deldir_2.0-4          
 #>  [88] survival_3.8-6         tidyselect_1.2.1       miniUI_0.1.2          
 #>  [91] pbapply_1.7-4          knitr_1.51             gridExtra_2.3         
 #>  [94] bookdown_0.46          scattermore_1.2        xfun_0.57             
-#>  [97] stringi_1.8.7          lazyeval_0.2.2         yaml_2.3.12           
+#>  [97] stringi_1.8.7          lazyeval_0.2.3         yaml_2.3.12           
 #> [100] evaluate_1.0.5         codetools_0.2-20       tibble_3.3.1          
-#> [103] BiocManager_1.30.27    cli_3.6.5              uwot_0.2.4            
-#> [106] xtable_1.8-8           reticulate_1.45.0      systemfonts_1.3.2     
+#> [103] BiocManager_1.30.27    cli_3.6.6              uwot_0.2.4            
+#> [106] xtable_1.8-8           reticulate_1.46.0      systemfonts_1.3.2     
 #> [109] jquerylib_0.1.4        Rcpp_1.1.1             spatstat.random_3.4-5 
 #> [112] globals_0.19.1         png_0.1-9              spatstat.univar_3.1-7 
 #> [115] parallel_4.5.3         pkgdown_2.2.0          ggplot2_4.0.2         
 #> [118] dotCall64_1.2          listenv_0.10.1         viridisLite_0.4.3     
 #> [121] scales_1.4.0           ggridges_0.5.7         purrr_1.2.1           
-#> [124] rlang_1.1.7            cowplot_1.2.0
+#> [124] rlang_1.2.0            cowplot_1.2.0
 ```

articles/anndataR.md

@@ -154,7 +154,7 @@ sessionInfo()
     ## [1] stats     graphics  grDevices utils     datasets  methods   base     
     ## 
     ## other attached packages:
-    ## [1] tidyr_1.3.2      dplyr_1.2.0      purrr_1.2.1      stringr_1.6.0   
+    ## [1] tidyr_1.3.2      dplyr_1.2.1      purrr_1.2.1      stringr_1.6.0   
     ## [5] rprojroot_2.1.1  knitr_1.51       tibble_3.3.1     BiocStyle_2.38.0
     ## 
     ## loaded via a namespace (and not attached):
@@ -163,10 +163,10 @@ sessionInfo()
     ##  [7] textshaping_1.0.5   yaml_2.3.12         fastmap_1.2.0      
     ## [10] R6_2.6.1            generics_0.1.4      htmlwidgets_1.6.4  
     ## [13] bookdown_0.46       desc_1.4.3          bslib_0.10.0       
-    ## [16] pillar_1.11.1       rlang_1.1.7         cachem_1.1.0       
+    ## [16] pillar_1.11.1       rlang_1.2.0         cachem_1.1.0       
     ## [19] stringi_1.8.7       xfun_0.57           fs_2.0.1           
-    ## [22] sass_0.4.10         otel_0.2.0          cli_3.6.5          
-    ## [25] pkgdown_2.2.0       withr_3.0.2         magrittr_2.0.4     
+    ## [22] sass_0.4.10         otel_0.2.0          cli_3.6.6          
+    ## [25] pkgdown_2.2.0       withr_3.0.2         magrittr_2.0.5     
     ## [28] digest_0.6.39       lifecycle_1.0.5     vctrs_0.7.2        
     ## [31] evaluate_1.0.5      glue_1.8.0          ragg_1.5.2         
     ## [34] rmarkdown_2.31      tools_4.5.3         pkgconfig_2.0.3    

articles/development_status.html

@@ -116,11 +116,11 @@ loaded via a namespace (and not attached):
  [1] digest_0.6.39       desc_1.4.3          R6_2.6.1           
  [4] bookdown_0.46       fastmap_1.2.0       xfun_0.57          
  [7] cachem_1.1.0        knitr_1.51          htmltools_0.5.9    
-[10] rmarkdown_2.31      lifecycle_1.0.5     cli_3.6.5          
+[10] rmarkdown_2.31      lifecycle_1.0.5     cli_3.6.6          
 [13] sass_0.4.10         pkgdown_2.2.0       textshaping_1.0.5  
 [16] jquerylib_0.1.4     systemfonts_1.3.2   compiler_4.5.3     
 [19] tools_4.5.3         ragg_1.5.2          bslib_0.10.0       
 [22] evaluate_1.0.5      yaml_2.3.12         BiocManager_1.30.27
-[25] otel_0.2.0          jsonlite_2.0.0      rlang_1.1.7        
+[25] otel_0.2.0          jsonlite_2.0.0      rlang_1.2.0        
 [28] fs_2.0.1            htmlwidgets_1.6.4  
 ```