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Auto-generated via `{sandpaper}`
Source  : 525d011
Branch  : main
Author  : Charlotte Soneson <[email protected]>
Time    : 2024-11-05 06:47:50 +0000
Message : Merge pull request #115 from carpentries-incubator/update/packages

Update 34 packages
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actions-user committed Nov 5, 2024
1 parent 276c7bd commit 1648954
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10 changes: 5 additions & 5 deletions 03-import-annotate.md
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Expand Up @@ -778,22 +778,22 @@ other attached packages:
[3] org.Mm.eg.db_3.19.1 AnnotationDbi_1.66.0
[5] SummarizedExperiment_1.34.0 Biobase_2.64.0
[7] MatrixGenerics_1.16.0 matrixStats_1.4.1
[9] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
[9] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1
[11] IRanges_2.38.1 S4Vectors_0.42.1
[13] BiocGenerics_0.50.0 knitr_1.48
loaded via a namespace (and not attached):
[1] Matrix_1.7-0 bit_4.5.0 jsonlite_1.8.9
[1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9
[4] highr_0.11 compiler_4.4.1 BiocManager_1.30.25
[7] renv_1.0.11 crayon_1.5.3 blob_1.2.4
[10] Biostrings_2.72.1 png_0.1-8 fastmap_1.2.0
[13] yaml_2.3.10 lattice_0.22-6 R6_2.5.1
[16] XVector_0.44.0 S4Arrays_1.4.1 DelayedArray_0.30.1
[19] GenomeInfoDbData_1.2.12 DBI_1.2.3 rlang_1.1.4
[22] KEGGREST_1.44.1 cachem_1.1.0 xfun_0.47
[25] bit64_4.0.5 memoise_2.0.1 SparseArray_1.4.8
[22] KEGGREST_1.44.1 cachem_1.1.0 xfun_0.49
[25] bit64_4.5.2 memoise_2.0.1 SparseArray_1.4.8
[28] RSQLite_2.3.7 cli_3.6.3 zlibbioc_1.50.0
[31] grid_4.4.1 vctrs_0.6.5 evaluate_1.0.0
[31] grid_4.4.1 vctrs_0.6.5 evaluate_1.0.1
[34] abind_1.4-8 httr_1.4.7 pkgconfig_2.0.3
[37] tools_4.4.1 UCSC.utils_1.0.0
```
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20 changes: 10 additions & 10 deletions 04-exploratory-qc.md
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Expand Up @@ -454,7 +454,7 @@ other attached packages:
[7] vsn_3.72.0 DESeq2_1.44.0
[9] SummarizedExperiment_1.34.0 Biobase_2.64.0
[11] MatrixGenerics_1.16.0 matrixStats_1.4.1
[13] GenomicRanges_1.56.1 GenomeInfoDb_1.40.1
[13] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1
[15] IRanges_2.38.1 S4Vectors_0.42.1
[17] BiocGenerics_0.50.0
Expand All @@ -464,32 +464,32 @@ loaded via a namespace (and not attached):
[7] mgcv_1.9-1 png_0.1-8 vctrs_0.6.5
[10] pkgconfig_2.0.3 shape_1.4.6.1 crayon_1.5.3
[13] fastmap_1.2.0 XVector_0.44.0 labeling_0.4.3
[16] utf8_1.2.4 promises_1.3.0 shinyAce_0.4.2
[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.47
[16] utf8_1.2.4 promises_1.3.0 shinyAce_0.4.3
[19] UCSC.utils_1.0.0 preprocessCore_1.66.0 xfun_0.49
[22] cachem_1.1.0 zlibbioc_1.50.0 jsonlite_1.8.9
[25] listviewer_4.0.0 highr_0.11 later_1.3.2
[28] DelayedArray_0.30.1 BiocParallel_1.38.0 parallel_4.4.1
[31] cluster_2.1.6 R6_2.5.1 bslib_0.8.0
[34] limma_3.60.4 jquerylib_0.1.4 Rcpp_1.0.13
[34] limma_3.60.6 jquerylib_0.1.4 Rcpp_1.0.13-1
[37] iterators_1.0.14 knitr_1.48 httpuv_1.6.15
[40] Matrix_1.7-0 splines_4.4.1 igraph_2.0.3
[40] Matrix_1.7-1 splines_4.4.1 igraph_2.1.1
[43] tidyselect_1.2.1 abind_1.4-8 yaml_2.3.10
[46] doParallel_1.0.17 codetools_0.2-20 affy_1.82.0
[49] miniUI_0.1.1.1 lattice_0.22-6 tibble_3.2.1
[52] shiny_1.9.1 withr_3.0.1 evaluate_1.0.0
[52] shiny_1.9.1 withr_3.0.2 evaluate_1.0.1
[55] circlize_0.4.16 pillar_1.9.0 affyio_1.74.0
[58] BiocManager_1.30.25 renv_1.0.11 DT_0.33
[61] foreach_1.5.2 shinyjs_2.1.0 generics_0.1.3
[64] munsell_0.5.1 scales_1.3.0 xtable_1.8-4
[67] glue_1.7.0 tools_4.4.1 colourpicker_1.3.0
[70] locfit_1.5-9.10 colorspace_2.1-1 nlme_3.1-164
[67] glue_1.8.0 tools_4.4.1 colourpicker_1.3.0
[70] locfit_1.5-9.10 colorspace_2.1-1 nlme_3.1-166
[73] GenomeInfoDbData_1.2.12 vipor_0.4.7 cli_3.6.3
[76] fansi_1.0.6 viridisLite_0.4.2 S4Arrays_1.4.1
[79] dplyr_1.1.4 gtable_0.3.5 rintrojs_0.3.4
[79] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4
[82] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8
[85] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23
[88] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4
[91] shinyWidgets_0.8.6 httr_1.4.7 GlobalOptions_0.1.2
[91] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2
[94] statmod_1.5.0 mime_0.12
```

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32 changes: 16 additions & 16 deletions 07-gene-set-analysis.md
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Expand Up @@ -500,9 +500,9 @@ microbenchmark(

``` output
Unit: microseconds
expr min lq mean median uq max neval
fisher 247.441 253.1220 287.03204 261.883 275.659 2133.728 100
hyper 1.453 1.6835 2.51601 1.999 3.061 9.678 100
expr min lq mean median uq max neval
fisher 240.809 245.127 266.64734 250.292 258.6875 1433.724 100
hyper 1.473 1.698 2.40966 2.625 2.8910 7.514 100
```

It is very astonishing that `phyper()` is hundreds of times faster than
Expand Down Expand Up @@ -1230,7 +1230,7 @@ resTimeGO = enrichGO(gene = timeDEgenes,
```

``` output
--> Expected input gene ID: 22702,16578,19113,192287,14211,210529
--> Expected input gene ID: 12380,99412,94221,18775,11674,378462
```

``` output
Expand Down Expand Up @@ -1478,19 +1478,19 @@ mmu00592 alpha-Linolenic acid metabolism - Mus mus
mmu04913 Ovarian steroidogenesis - Mus musculus (house mouse)
mmu04061 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)
GeneRatio BgRatio RichFactor FoldEnrichment zScore pvalue
mmu00590 16/460 89/9787 0.1797753 3.824915 5.945245 3.232256e-06
mmu00591 12/460 55/9787 0.2181818 4.642055 6.015024 6.976725e-06
mmu00565 11/460 48/9787 0.2291667 4.875770 5.977670 1.021306e-05
mmu00592 8/460 25/9787 0.3200000 6.808348 6.457490 1.194030e-05
mmu04913 12/460 64/9787 0.1875000 3.989266 5.328009 3.553165e-05
mmu04061 14/460 95/9787 0.1473684 3.135423 4.644614 1.301689e-04
mmu00590 16/454 89/9709 0.1797753 3.844578 5.970763 3.021082e-06
mmu00591 12/454 55/9709 0.2181818 4.665919 6.038307 6.615368e-06
mmu00565 11/454 48/9709 0.2291667 4.900835 6.000284 9.722179e-06
mmu00592 8/454 25/9709 0.3200000 6.843348 6.479015 1.149555e-05
mmu04913 12/454 64/9709 0.1875000 4.009774 5.350291 3.376203e-05
mmu04061 14/454 95/9709 0.1473684 3.151542 4.667283 1.232101e-04
p.adjust qvalue
mmu00590 0.0009253733 0.0008012571
mmu00591 0.0009253733 0.0008012571
mmu00565 0.0009253733 0.0008012571
mmu00592 0.0009253733 0.0008012571
mmu04913 0.0022029625 0.0019074887
mmu04061 0.0067253926 0.0058233450
mmu00590 0.0008794095 0.0007593113
mmu00591 0.0008794095 0.0007593113
mmu00565 0.0008794095 0.0007593113
mmu00592 0.0008794095 0.0007593113
mmu04913 0.0020662361 0.0017840566
mmu04061 0.0062837135 0.0054255662
geneID
mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
mmu00591 18783/211429/329502/78390/242546/18781/18784/13113/622127/232889/237625/11687
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86 changes: 0 additions & 86 deletions config.yaml
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36 changes: 18 additions & 18 deletions md5sum.txt
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@@ -1,19 +1,19 @@
"file" "checksum" "built" "date"
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