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Auto-generated via `{sandpaper}`
Source  : bee1529
Branch  : main
Author  : Charlotte Soneson <charlottesoneson@gmail.com>
Time    : 2025-01-07 07:36:38 +0000
Message : Merge pull request #118 from carpentries-incubator/update/packages

Update 21 packages
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actions-user committed Jan 7, 2025
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4 changes: 2 additions & 2 deletions 03-import-annotate.md
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Expand Up @@ -783,15 +783,15 @@ other attached packages:
[13] BiocGenerics_0.50.0 knitr_1.49
loaded via a namespace (and not attached):
[1] Matrix_1.7-1 bit_4.5.0 jsonlite_1.8.9
[1] Matrix_1.7-1 bit_4.5.0.1 jsonlite_1.8.9
[4] compiler_4.4.2 BiocManager_1.30.25 renv_1.0.11
[7] crayon_1.5.3 blob_1.2.4 Biostrings_2.72.1
[10] png_0.1-8 fastmap_1.2.0 yaml_2.3.10
[13] lattice_0.22-6 R6_2.5.1 XVector_0.44.0
[16] S4Arrays_1.4.1 DelayedArray_0.30.1 GenomeInfoDbData_1.2.12
[19] DBI_1.2.3 rlang_1.1.4 KEGGREST_1.44.1
[22] cachem_1.1.0 xfun_0.49 bit64_4.5.2
[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.8
[25] memoise_2.0.1 SparseArray_1.4.8 RSQLite_2.3.9
[28] cli_3.6.3 zlibbioc_1.50.0 grid_4.4.2
[31] vctrs_0.6.5 evaluate_1.0.1 abind_1.4-8
[34] httr_1.4.7 pkgconfig_2.0.3 tools_4.4.2
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53 changes: 26 additions & 27 deletions 04-exploratory-qc.md
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Expand Up @@ -464,33 +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_1.3.2 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 later_1.4.1 DelayedArray_0.30.1
[28] BiocParallel_1.38.0 parallel_4.4.2 cluster_2.1.6
[31] R6_2.5.1 bslib_0.8.0 limma_3.60.6
[34] jquerylib_0.1.4 Rcpp_1.0.13-1 iterators_1.0.14
[37] knitr_1.49 httpuv_1.6.15 Matrix_1.7-1
[40] splines_4.4.2 igraph_2.1.1 tidyselect_1.2.1
[43] abind_1.4-8 yaml_2.3.10 doParallel_1.0.17
[46] codetools_0.2-20 affy_1.82.0 miniUI_0.1.1.1
[49] lattice_0.22-6 tibble_3.2.1 shiny_1.9.1
[52] withr_3.0.2 evaluate_1.0.1 circlize_0.4.16
[55] pillar_1.9.0 affyio_1.74.0 BiocManager_1.30.25
[58] renv_1.0.11 DT_0.33 foreach_1.5.2
[61] shinyjs_2.1.0 generics_0.1.3 munsell_0.5.1
[64] scales_1.3.0 xtable_1.8-4 glue_1.8.0
[67] tools_4.4.2 colourpicker_1.3.0 locfit_1.5-9.10
[70] colorspace_2.1-1 nlme_3.1-166 GenomeInfoDbData_1.2.12
[73] vipor_0.4.7 cli_3.6.3 fansi_1.0.6
[76] viridisLite_0.4.2 S4Arrays_1.4.1 dplyr_1.1.4
[79] gtable_0.3.6 rintrojs_0.3.4 sass_0.4.9
[82] digest_0.6.37 SparseArray_1.4.8 ggrepel_0.9.6
[85] farver_2.1.2 rjson_0.2.23 htmlwidgets_1.6.4
[88] htmltools_0.5.8.1 lifecycle_1.0.4 shinyWidgets_0.8.7
[91] httr_1.4.7 GlobalOptions_0.1.2 statmod_1.5.0
[94] mime_0.12
[16] promises_1.3.2 shinyAce_0.4.3 UCSC.utils_1.0.0
[19] preprocessCore_1.66.0 xfun_0.49 cachem_1.1.0
[22] zlibbioc_1.50.0 jsonlite_1.8.9 listviewer_4.0.0
[25] later_1.4.1 DelayedArray_0.30.1 BiocParallel_1.38.0
[28] parallel_4.4.2 cluster_2.1.8 R6_2.5.1
[31] bslib_0.8.0 limma_3.60.6 jquerylib_0.1.4
[34] Rcpp_1.0.13-1 iterators_1.0.14 knitr_1.49
[37] httpuv_1.6.15 Matrix_1.7-1 splines_4.4.2
[40] igraph_2.1.2 tidyselect_1.2.1 abind_1.4-8
[43] yaml_2.3.10 doParallel_1.0.17 codetools_0.2-20
[46] affy_1.82.0 miniUI_0.1.1.1 lattice_0.22-6
[49] tibble_3.2.1 shiny_1.10.0 withr_3.0.2
[52] evaluate_1.0.1 circlize_0.4.16 pillar_1.10.0
[55] affyio_1.74.0 BiocManager_1.30.25 renv_1.0.11
[58] DT_0.33 foreach_1.5.2 shinyjs_2.1.0
[61] generics_0.1.3 munsell_0.5.1 scales_1.3.0
[64] xtable_1.8-4 glue_1.8.0 tools_4.4.2
[67] colourpicker_1.3.0 locfit_1.5-9.10 colorspace_2.1-1
[70] nlme_3.1-166 GenomeInfoDbData_1.2.12 vipor_0.4.7
[73] cli_3.6.3 viridisLite_0.4.2 S4Arrays_1.4.1
[76] dplyr_1.1.4 gtable_0.3.6 rintrojs_0.3.4
[79] sass_0.4.9 digest_0.6.37 SparseArray_1.4.8
[82] ggrepel_0.9.6 farver_2.1.2 rjson_0.2.23
[85] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4
[88] shinyWidgets_0.8.7 httr_1.4.7 GlobalOptions_0.1.2
[91] statmod_1.5.0 mime_0.12
```

:::::::::::::::::::::::::::::::::::::::: keypoints
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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 242.563 244.937 262.70772 247.967 251.9505 1406.496 100
hyper 1.492 1.693 2.33685 2.555 2.8555 6.101 100
expr min lq mean median uq max neval
fisher 242.642 249.1445 271.24591 252.195 262.1435 1561.651 100
hyper 1.473 1.7080 2.53325 2.720 2.9710 8.786 100
```

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: 73884,382007,13214,226356,208188,66197
--> Expected input gene ID: 60597,11517,17864,100039030,54486,69496
```

``` 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 89/9818 0.1797753 3.837030 5.960759 3.104291e-06
mmu00591 12/460 55/9818 0.2181818 4.656759 6.029243 6.756868e-06
mmu00565 11/460 48/9818 0.2291667 4.891214 5.991495 9.914058e-06
mmu00592 8/460 25/9818 0.3200000 6.829913 6.470696 1.166851e-05
mmu04913 12/460 64/9818 0.1875000 4.001902 5.341607 3.445424e-05
mmu04061 14/460 95/9818 0.1473684 3.145355 4.658408 1.259362e-04
mmu00590 16/451 89/9569 0.1797753 3.814345 5.932220 3.338144e-06
mmu00591 12/451 55/9569 0.2181818 4.629228 6.002927 7.161290e-06
mmu00565 11/451 48/9569 0.2291667 4.862297 5.965873 1.046503e-05
mmu00592 8/451 25/9569 0.3200000 6.789534 6.446107 1.217181e-05
mmu04913 12/451 64/9569 0.1875000 3.978243 5.316467 3.643828e-05
mmu04061 14/451 95/9569 0.1473684 3.126759 4.633002 1.337191e-04
p.adjust qvalue
mmu00590 0.0009101439 0.0007860892
mmu00591 0.0009101439 0.0007860892
mmu00565 0.0009101439 0.0007860892
mmu00592 0.0009101439 0.0007860892
mmu04913 0.0021499443 0.0018569019
mmu04061 0.0065486813 0.0056560810
mmu00590 0.0009494012 0.0008231987
mmu00591 0.0009494012 0.0008231987
mmu00565 0.0009494012 0.0008231987
mmu00592 0.0009494012 0.0008231987
mmu04913 0.0022737489 0.0019715029
mmu04061 0.0069533935 0.0060290895
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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