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Auto-generated via {sandpaper}
Source  : 620e18d
Branch  : main
Author  : Charlotte Soneson <[email protected]>
Time    : 2024-01-02 07:40:08 +0000
Message : Merge pull request #99 from carpentries-incubator/update/packages

Update 44 packages
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actions-user committed Jan 2, 2024
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14 changes: 7 additions & 7 deletions 03-import-annotate.md
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Expand Up @@ -777,23 +777,23 @@ other attached packages:
[1] hgu95av2.db_3.13.0 org.Hs.eg.db_3.17.0
[3] org.Mm.eg.db_3.17.0 AnnotationDbi_1.62.2
[5] SummarizedExperiment_1.30.2 Biobase_2.60.0
[7] MatrixGenerics_1.12.3 matrixStats_1.0.0
[7] MatrixGenerics_1.12.3 matrixStats_1.2.0
[9] GenomicRanges_1.52.1 GenomeInfoDb_1.36.4
[11] IRanges_2.34.1 S4Vectors_0.38.2
[13] BiocGenerics_0.46.0 knitr_1.45
loaded via a namespace (and not attached):
[1] Matrix_1.6-1.1 bit_4.0.5 highr_0.10
[1] Matrix_1.6-4 bit_4.0.5 highr_0.10
[4] compiler_4.3.2 BiocManager_1.30.22 renv_1.0.3
[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_2.3.7 lattice_0.22-5 R6_2.5.1
[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_1.1.3 rlang_1.1.2
[19] GenomeInfoDbData_1.2.10 DBI_1.2.0 rlang_1.1.2
[22] KEGGREST_1.40.1 cachem_1.0.8 xfun_0.41
[25] bit64_4.0.5 RSQLite_2.3.3 memoise_2.0.1
[28] cli_3.6.1 zlibbioc_1.46.0 grid_4.3.2
[31] vctrs_0.6.4 evaluate_0.23 abind_1.4-5
[25] bit64_4.0.5 RSQLite_2.3.4 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
[34] RCurl_1.98-1.13 httr_1.4.7 pkgconfig_2.0.3
[37] tools_4.3.2
```
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32 changes: 16 additions & 16 deletions 04-exploratory-qc.md
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Expand Up @@ -427,42 +427,42 @@ other attached packages:
[5] ComplexHeatmap_2.16.0 ggplot2_3.4.4
[7] vsn_3.68.0 DESeq2_1.40.2
[9] SummarizedExperiment_1.30.2 Biobase_2.60.0
[11] MatrixGenerics_1.12.3 matrixStats_1.0.0
[11] MatrixGenerics_1.12.3 matrixStats_1.2.0
[13] GenomicRanges_1.52.1 GenomeInfoDb_1.36.4
[15] IRanges_2.34.1 S4Vectors_0.38.2
[17] BiocGenerics_0.46.0
loaded via a namespace (and not attached):
[1] bitops_1.0-7 rlang_1.1.2 magrittr_2.0.3
[4] shinydashboard_0.7.2 clue_0.3-65 GetoptLong_1.0.5
[7] compiler_4.3.2 mgcv_1.9-0 png_0.1-8
[10] vctrs_0.6.4 pkgconfig_2.0.3 shape_1.4.6
[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
[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
[25] jsonlite_1.8.7 highr_0.10 later_1.3.1
[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_2.1.4 R6_2.5.1 bslib_0.5.1
[31] cluster_2.1.6 R6_2.5.1 bslib_0.6.1
[34] limma_3.56.2 jquerylib_0.1.4 Rcpp_1.0.11
[37] iterators_1.0.14 knitr_1.45 httpuv_1.6.12
[40] Matrix_1.6-1.1 splines_4.3.2 igraph_1.5.1
[43] tidyselect_1.2.0 abind_1.4-5 yaml_2.3.7
[37] iterators_1.0.14 knitr_1.45 httpuv_1.6.13
[40] Matrix_1.6-4 splines_4.3.2 igraph_1.6.0
[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_1.7.5.1 withr_2.5.2 evaluate_0.23
[52] shiny_1.8.0 withr_2.5.2 evaluate_0.23
[55] circlize_0.4.15 pillar_1.9.0 affyio_1.70.0
[58] BiocManager_1.30.22 renv_1.0.3 DT_0.30
[58] BiocManager_1.30.22 renv_1.0.3 DT_0.31
[61] foreach_1.5.2 shinyjs_2.1.0 generics_0.1.3
[64] RCurl_1.98-1.13 munsell_0.5.0 scales_1.2.1
[64] RCurl_1.98-1.13 munsell_0.5.0 scales_1.3.0
[67] xtable_1.8-4 glue_1.6.2 tools_4.3.2
[70] colourpicker_1.3.0 locfit_1.5-9.8 colorspace_2.1-0
[73] nlme_3.1-163 GenomeInfoDbData_1.2.10 vipor_0.4.5
[76] cli_3.6.1 fansi_1.0.5 viridisLite_0.4.2
[79] S4Arrays_1.0.6 dplyr_1.1.3 gtable_0.3.4
[82] rintrojs_0.3.3 sass_0.4.7 digest_0.6.33
[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_0.3.3 sass_0.4.8 digest_0.6.33
[85] ggrepel_0.9.4 farver_2.1.1 rjson_0.2.21
[88] htmlwidgets_1.6.2 htmltools_0.5.7 lifecycle_1.0.3
[88] htmlwidgets_1.6.4 htmltools_0.5.7 lifecycle_1.0.4
[91] shinyWidgets_0.8.0 GlobalOptions_0.1.2 mime_0.12
```

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20 changes: 10 additions & 10 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 238.465 243.715 252.68149 246.8705 252.3760 488.411 100
hyper 1.352 1.543 2.23699 2.5545 2.8355 5.901 100
expr min lq mean median uq max neval
fisher 238.455 241.8405 250.98679 244.1705 251.2475 552.429 100
hyper 1.332 1.5180 2.38207 2.5445 2.8055 17.983 100
```

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: 76867,320214,23797,110355,217011,103583
--> Expected input gene ID: 20317,622554,21681,105988,67000,239731
```

```{.output}
Expand Down Expand Up @@ -1471,12 +1471,12 @@ mmu00591 Linoleic 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 pvalue p.adjust qvalue
mmu00590 16/454 85/9392 2.456998e-06 0.0007542983 0.0006620963
mmu00565 11/454 48/9392 1.327107e-05 0.0014975168 0.0013144670
mmu00592 8/454 25/9392 1.463371e-05 0.0014975168 0.0013144670
mmu00591 11/454 50/9392 2.009867e-05 0.0015425732 0.0013540159
mmu04913 12/454 63/9392 3.956222e-05 0.0024291201 0.0021321953
mmu04061 14/454 95/9392 1.740468e-04 0.0079696743 0.0069954967
mmu00590 16/454 85/9408 2.403809e-06 0.0007379694 0.0006452329
mmu00565 11/454 48/9408 1.306159e-05 0.0014791271 0.0012932536
mmu00592 8/454 25/9408 1.445401e-05 0.0014791271 0.0012932536
mmu00591 11/454 50/9408 1.978440e-05 0.0015184527 0.0013276373
mmu04913 12/454 63/9408 3.891349e-05 0.0023892882 0.0020890399
mmu04061 14/454 95/9408 1.710081e-04 0.0078109667 0.0068294068
geneID
mmu00590 18783/19215/211429/329502/78390/19223/67103/242546/13118/18781/18784/11689/232889/15446/237625/11687
mmu00565 18783/211429/329502/78390/22239/18781/18784/232889/320981/237625/53897
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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 @@
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