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Auto-generated via {sandpaper} Source : f52e1be Branch : main Author : Jenny Drnevich <drnevich@illinois.edu> Time : 2024-03-05 02:13:52 +0000 Message : Merge pull request #103 from carpentries-incubator/update/packages Update 24 packages
carpentries-incubator · Mar 5, 2024 · 2179b56 · 2179b56
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diff --git a/03-import-annotate.md b/03-import-annotate.md
@@ -784,13 +784,13 @@ other attached packages:
 
 loaded via a namespace (and not attached):
  [1] Matrix_1.6-5            bit_4.0.5               highr_0.10             
- [4] compiler_4.3.2          BiocManager_1.30.22     renv_1.0.4             
+ [4] compiler_4.3.2          BiocManager_1.30.22     renv_1.0.5             
  [7] crayon_1.5.2            blob_1.2.4              Biostrings_2.68.1      
 [10] bitops_1.0-7            png_0.1-8               fastmap_1.1.1          
 [13] yaml_2.3.8              lattice_0.22-5          R6_2.5.1               
 [16] XVector_0.40.0          S4Arrays_1.0.6          DelayedArray_0.26.7    
-[19] GenomeInfoDbData_1.2.10 DBI_1.2.1               rlang_1.1.3            
-[22] KEGGREST_1.40.1         cachem_1.0.8            xfun_0.41              
+[19] GenomeInfoDbData_1.2.10 DBI_1.2.2               rlang_1.1.3            
+[22] KEGGREST_1.40.1         cachem_1.0.8            xfun_0.42              
 [25] bit64_4.0.5             RSQLite_2.3.5           memoise_2.0.1          
 [28] cli_3.6.2               zlibbioc_1.46.0         grid_4.3.2             
 [31] vctrs_0.6.5             evaluate_0.23           abind_1.4-5            

diff --git a/04-exploratory-qc.md b/04-exploratory-qc.md
@@ -424,7 +424,7 @@ attached base packages:
 other attached packages:
  [1] iSEE_2.12.0                 SingleCellExperiment_1.22.0
  [3] hexbin_1.28.3               RColorBrewer_1.1-3         
- [5] ComplexHeatmap_2.16.0       ggplot2_3.4.4              
+ [5] ComplexHeatmap_2.16.0       ggplot2_3.5.0              
  [7] vsn_3.68.0                  DESeq2_1.40.2              
  [9] SummarizedExperiment_1.30.2 Biobase_2.60.0             
 [11] MatrixGenerics_1.12.3       matrixStats_1.2.0          
@@ -436,34 +436,34 @@ loaded via a namespace (and not attached):
  [1] bitops_1.0-7            rlang_1.1.3             magrittr_2.0.3         
  [4] shinydashboard_0.7.2    clue_0.3-65             GetoptLong_1.0.5       
  [7] compiler_4.3.2          mgcv_1.9-1              png_0.1-8              
-[10] vctrs_0.6.5             pkgconfig_2.0.3         shape_1.4.6            
+[10] vctrs_0.6.5             pkgconfig_2.0.3         shape_1.4.6.1          
 [13] crayon_1.5.2            fastmap_1.1.1           XVector_0.40.0         
 [16] ellipsis_0.3.2          labeling_0.4.3          utf8_1.2.4             
 [19] promises_1.2.1          preprocessCore_1.62.1   shinyAce_0.4.2         
-[22] xfun_0.41               cachem_1.0.8            zlibbioc_1.46.0        
+[22] xfun_0.42               cachem_1.0.8            zlibbioc_1.46.0        
 [25] jsonlite_1.8.8          highr_0.10              later_1.3.2            
 [28] DelayedArray_0.26.7     BiocParallel_1.34.2     parallel_4.3.2         
 [31] cluster_2.1.6           R6_2.5.1                bslib_0.6.1            
 [34] limma_3.56.2            jquerylib_0.1.4         Rcpp_1.0.12            
 [37] iterators_1.0.14        knitr_1.45              httpuv_1.6.14          
-[40] Matrix_1.6-5            splines_4.3.2           igraph_2.0.1.1         
+[40] Matrix_1.6-5            splines_4.3.2           igraph_2.0.2           
 [43] tidyselect_1.2.0        abind_1.4-5             yaml_2.3.8             
 [46] doParallel_1.0.17       codetools_0.2-19        affy_1.78.2            
 [49] miniUI_0.1.1.1          lattice_0.22-5          tibble_3.2.1           
 [52] shiny_1.8.0             withr_3.0.0             evaluate_0.23          
-[55] circlize_0.4.15         pillar_1.9.0            affyio_1.70.0          
-[58] BiocManager_1.30.22     renv_1.0.4              DT_0.31                
+[55] circlize_0.4.16         pillar_1.9.0            affyio_1.70.0          
+[58] BiocManager_1.30.22     renv_1.0.5              DT_0.32                
 [61] foreach_1.5.2           shinyjs_2.1.0           generics_0.1.3         
 [64] RCurl_1.98-1.14         munsell_0.5.0           scales_1.3.0           
 [67] xtable_1.8-4            glue_1.7.0              tools_4.3.2            
-[70] colourpicker_1.3.0      locfit_1.5-9.8          colorspace_2.1-0       
+[70] colourpicker_1.3.0      locfit_1.5-9.9          colorspace_2.1-0       
 [73] nlme_3.1-164            GenomeInfoDbData_1.2.10 vipor_0.4.7            
 [76] cli_3.6.2               fansi_1.0.6             viridisLite_0.4.2      
 [79] S4Arrays_1.0.6          dplyr_1.1.4             gtable_0.3.4           
 [82] rintrojs_0.3.4          sass_0.4.8              digest_0.6.34          
 [85] ggrepel_0.9.5           farver_2.1.1            rjson_0.2.21           
 [88] htmlwidgets_1.6.4       htmltools_0.5.7         lifecycle_1.0.4        
-[91] shinyWidgets_0.8.1      GlobalOptions_0.1.2     mime_0.12              
+[91] shinyWidgets_0.8.2      GlobalOptions_0.1.2     mime_0.12              
 ```
 
 :::::::::::::::::::::::::::::::::::::::: keypoints

diff --git a/07-gene-set-analysis.md b/07-gene-set-analysis.md
@@ -500,9 +500,9 @@ microbenchmark(
 
 ```{.output}
 Unit: microseconds
-   expr     min      lq      mean  median      uq     max neval
- fisher 238.395 247.371 259.92009 251.464 261.573 469.346   100
-  hyper   1.362   1.553   2.44718   2.615   2.825  17.543   100
+   expr     min      lq      mean  median       uq      max neval
+ fisher 238.955 243.980 270.67608 248.163 259.2635 1920.491   100
+  hyper   1.333   1.488   2.28346   2.550   2.8505    6.953   100
 ```
 
 It is very astonishing that `phyper()` is hundreds of times faster than
@@ -1230,7 +1230,7 @@ resTimeGO = enrichGO(gene = timeDEgenes,
 ```
 
 ```{.output}
---> Expected input gene ID: 12235,19701,13874,16882,235036,245944
+--> Expected input gene ID: 23920,12589,22068,330470,21808,74716
 ```
 
 ```{.output}

diff --git a/config.yaml b/config.yaml
diff --git a/fig/04-exploratory-qc-rendered-pca-exercise-1.png b/fig/04-exploratory-qc-rendered-pca-exercise-1.png
diff --git a/fig/05-differential-expression-rendered-heatmap-time-1.png b/fig/05-differential-expression-rendered-heatmap-time-1.png
diff --git a/fig/07-gene-set-analysis-rendered-hypergeom-1.png b/fig/07-gene-set-analysis-rendered-hypergeom-1.png
diff --git a/fig/07-gene-set-analysis-rendered-more-enrichplots-1.png b/fig/07-gene-set-analysis-rendered-more-enrichplots-1.png
diff --git a/fig/07-gene-set-analysis-rendered-more-enrichplots-2.png b/fig/07-gene-set-analysis-rendered-more-enrichplots-2.png
diff --git a/fig/07-gene-set-analysis-rendered-plot-enrichment-padj-1.png b/fig/07-gene-set-analysis-rendered-plot-enrichment-padj-1.png
diff --git a/fig/07-gene-set-analysis-rendered-plot-up-down-1.png b/fig/07-gene-set-analysis-rendered-plot-up-down-1.png
diff --git a/fig/07-gene-set-analysis-rendered-plot-z-1.png b/fig/07-gene-set-analysis-rendered-plot-z-1.png
diff --git a/md5sum.txt b/md5sum.txt
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