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Auto-generated via {sandpaper}
Source  : b28586e
Branch  : main
Author  : Charlotte Soneson <charlottesoneson@gmail.com>
Time    : 2023-11-07 06:42:38 +0000
Message : Merge pull request #97 from carpentries-incubator/update/packages

Update 48 packages
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actions-user committed Nov 7, 2023
1 parent a454910 commit 22a0204
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20 changes: 10 additions & 10 deletions 03-import-annotate.md
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Expand Up @@ -778,23 +778,23 @@ other attached packages:
[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
[9] GenomicRanges_1.52.0 GenomeInfoDb_1.36.2
[11] IRanges_2.34.1 S4Vectors_0.38.1
[13] BiocGenerics_0.46.0 knitr_1.43
[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 bit_4.0.5 highr_0.10
[1] Matrix_1.6-1.1 bit_4.0.5 highr_0.10
[4] compiler_4.3.1 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_0.21-8 R6_2.5.1
[13] yaml_2.3.7 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_1.1.1
[22] KEGGREST_1.40.0 cachem_1.0.8 xfun_0.40
[25] bit64_4.0.5 RSQLite_2.3.1 memoise_2.0.1
[19] GenomeInfoDbData_1.2.10 DBI_1.1.3 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_4.3.1
[31] vctrs_0.6.3 evaluate_0.21 abind_1.4-5
[34] RCurl_1.98-1.12 httr_1.4.7 pkgconfig_2.0.3
[31] vctrs_0.6.4 evaluate_0.23 abind_1.4-5
[34] RCurl_1.98-1.13 httr_1.4.7 pkgconfig_2.0.3
[37] tools_4.3.1
```

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36 changes: 18 additions & 18 deletions 04-exploratory-qc.md
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Expand Up @@ -424,45 +424,45 @@ 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_3.4.3
[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
[13] GenomicRanges_1.52.0 GenomeInfoDb_1.36.2
[15] IRanges_2.34.1 S4Vectors_0.38.1
[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_1.1.1 magrittr_2.0.3
[4] shinydashboard_0.7.2 clue_0.3-64 GetoptLong_1.0.5
[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_4.3.1 mgcv_1.9-0 png_0.1-8
[10] vctrs_0.6.3 pkgconfig_2.0.3 shape_1.4.6
[10] vctrs_0.6.4 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_1.2.3
[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_0.40 cachem_1.0.8 zlibbioc_1.46.0
[22] xfun_0.41 cachem_1.0.8 zlibbioc_1.46.0
[25] jsonlite_1.8.7 highr_0.10 later_1.3.1
[28] DelayedArray_0.26.7 BiocParallel_1.34.2 parallel_4.3.1
[31] cluster_2.1.4 R6_2.5.1 bslib_0.5.1
[34] limma_3.56.2 jquerylib_0.1.4 Rcpp_1.0.11
[37] iterators_1.0.14 knitr_1.43 httpuv_1.6.11
[40] Matrix_1.6-1 splines_4.3.1 igraph_1.5.1
[37] iterators_1.0.14 knitr_1.45 httpuv_1.6.12
[40] Matrix_1.6-1.1 splines_4.3.1 igraph_1.5.1
[43] tidyselect_1.2.0 abind_1.4-5 yaml_2.3.7
[46] doParallel_1.0.17 codetools_0.2-19 affy_1.78.2
[49] miniUI_0.1.1.1 lattice_0.21-8 tibble_3.2.1
[52] shiny_1.7.5 withr_2.5.0 evaluate_0.21
[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
[55] circlize_0.4.15 pillar_1.9.0 affyio_1.70.0
[58] BiocManager_1.30.22 renv_1.0.3 DT_0.29
[58] BiocManager_1.30.22 renv_1.0.3 DT_0.30
[61] foreach_1.5.2 shinyjs_2.1.0 generics_0.1.3
[64] RCurl_1.98-1.12 munsell_0.5.0 scales_1.2.1
[64] RCurl_1.98-1.13 munsell_0.5.0 scales_1.2.1
[67] xtable_1.8-4 glue_1.6.2 tools_4.3.1
[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_1.0.4 viridisLite_0.4.2
[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_0.3.2 sass_0.4.7 digest_0.6.33
[85] ggrepel_0.9.3 farver_2.1.1 rjson_0.2.21
[88] htmlwidgets_1.6.2 htmltools_0.5.6 lifecycle_1.0.3
[82] rintrojs_0.3.3 sass_0.4.7 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
[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 @@ -501,8 +501,8 @@ microbenchmark(
```{.output}
Unit: microseconds
expr min lq mean median uq max neval
fisher 285.4 291.1 303.952 297.05 307.55 542.8 100
hyper 1.6 1.8 2.560 2.35 2.80 19.9 100
fisher 282.4 288.6 300.440 293.35 303.65 552.9 100
hyper 1.7 1.8 2.585 2.40 2.80 20.8 100
```

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: 19017,320752,239528,14610,20779,14725
--> Expected input gene ID: 11498,268903,217116,320558,83560,225182
```

```{.output}
Expand Down Expand Up @@ -1470,13 +1470,13 @@ mmu00592 alpha-Linolenic acid metabolism - Mus mus
mmu00591 Linoleic acid metabolism - Mus musculus (house mouse)
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 16/452 85/9334 2.512075e-06 0.0007686949 0.0006795824
mmu00565 11/452 48/9334 1.348878e-05 0.0015117273 0.0013364772
mmu00592 8/452 25/9334 1.482086e-05 0.0015117273 0.0013364772
mmu00591 11/452 50/9334 2.042533e-05 0.0015625374 0.0013813971
mmu04913 12/452 63/9334 4.023622e-05 0.0024624567 0.0021769913
mmu04061 14/452 95/9334 1.772022e-04 0.0081077454 0.0071678382
GeneRatio BgRatio pvalue p.adjust qvalue
mmu00590 16/454 85/9391 2.460363e-06 0.0007553315 0.000665593
mmu00565 11/454 48/9391 1.328428e-05 0.0014986747 0.001320622
mmu00592 8/454 25/9391 1.464503e-05 0.0014986747 0.001320622
mmu00591 11/454 50/9391 2.011850e-05 0.0015440945 0.001360646
mmu04913 12/454 63/9391 3.960315e-05 0.0024316333 0.002142739
mmu04061 14/454 95/9391 1.742386e-04 0.0079797049 0.007031662
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 @@
"file" "checksum" "built" "date"
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