Skip to content

Commit

Permalink
markdown source builds
Browse files Browse the repository at this point in the history 
Auto-generated via {sandpaper}
Source  : 047cf62
Branch  : main
Author  : Charlotte Soneson <[email protected]>
Time    : 2023-09-05 17:19:07 +0000
Message : Merge pull request #79 from carpentries-incubator/znk/update/packages

update 50 packages
  • Loading branch information
@actions-user
actions-user committed Sep 5, 2023
1 parent 9ec972c commit 3c789c8
Show file tree
Hide file tree
Showing 12 changed files with 48 additions and 2,895 deletions.
17 changes: 9 additions & 8 deletions 03-import-annotate.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -714,24 +714,25 @@ 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_1.12.2 matrixStats_1.0.0
[9] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1
[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
loaded via a namespace (and not attached):
[1] Matrix_1.5-4.1 bit_4.0.5 highr_0.10
[4] compiler_4.3.1 BiocManager_1.30.21 renv_1.0.2
[1] Matrix_1.6-1 bit_4.0.5 highr_0.10
[4] compiler_4.3.1 BiocManager_1.30.22 renv_1.0.2
[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
[16] XVector_0.40.0 S4Arrays_1.0.4 DelayedArray_0.26.6
[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_0.39
[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
[28] cli_3.6.1 zlibbioc_1.46.0 grid_4.3.1
[31] vctrs_0.6.3 evaluate_0.21 RCurl_1.98-1.12
[34] httr_1.4.6 pkgconfig_2.0.3 tools_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
[37] tools_4.3.1
```

::: keypoints
Expand Down
34 changes: 17 additions & 17 deletions 04-exploratory-qc.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -284,36 +284,36 @@ attached base packages:
other attached packages:
[1] hexbin_1.28.3 RColorBrewer_1.1-3
[3] ComplexHeatmap_2.16.0 ggplot2_3.4.2
[3] ComplexHeatmap_2.16.0 ggplot2_3.4.3
[5] vsn_3.68.0 DESeq2_1.40.2
[7] SummarizedExperiment_1.30.2 Biobase_2.60.0
[9] MatrixGenerics_1.12.2 matrixStats_1.0.0
[11] GenomicRanges_1.52.0 GenomeInfoDb_1.36.1
[9] MatrixGenerics_1.12.3 matrixStats_1.0.0
[11] GenomicRanges_1.52.0 GenomeInfoDb_1.36.2
[13] IRanges_2.34.1 S4Vectors_0.38.1
[15] BiocGenerics_0.46.0
loaded via a namespace (and not attached):
[1] shape_1.4.6 circlize_0.4.15 gtable_0.3.3
[4] rjson_0.2.21 xfun_0.39 GlobalOptions_0.1.2
[1] shape_1.4.6 circlize_0.4.15 gtable_0.3.4
[4] rjson_0.2.21 xfun_0.40 GlobalOptions_0.1.2
[7] lattice_0.21-8 vctrs_0.6.3 tools_4.3.1
[10] bitops_1.0-7 generics_0.1.3 parallel_4.3.1
[13] tibble_3.2.1 fansi_1.0.4 highr_0.10
[16] cluster_2.1.4 pkgconfig_2.0.3 Matrix_1.5-4.1
[16] cluster_2.1.4 pkgconfig_2.0.3 Matrix_1.6-1
[19] lifecycle_1.0.3 GenomeInfoDbData_1.2.10 farver_2.1.1
[22] compiler_4.3.1 munsell_0.5.0 codetools_0.2-19
[25] clue_0.3-64 RCurl_1.98-1.12 yaml_2.3.7
[28] preprocessCore_1.62.1 pillar_1.9.0 crayon_1.5.2
[31] BiocParallel_1.34.2 affy_1.78.0 DelayedArray_0.26.6
[34] limma_3.56.2 iterators_1.0.14 foreach_1.5.2
[37] tidyselect_1.2.0 locfit_1.5-9.8 digest_0.6.33
[40] dplyr_1.1.2 labeling_0.4.2 colorspace_2.1-0
[43] cli_3.6.1 magrittr_2.0.3 S4Arrays_1.0.4
[46] utf8_1.2.3 withr_2.5.0 scales_1.2.1
[49] XVector_0.40.0 affyio_1.70.0 GetoptLong_1.0.5
[52] png_0.1-8 evaluate_0.21 knitr_1.43
[55] doParallel_1.0.17 rlang_1.1.1 Rcpp_1.0.11
[58] glue_1.6.2 BiocManager_1.30.21 renv_1.0.2
[61] R6_2.5.1 zlibbioc_1.46.0
[31] BiocParallel_1.34.2 affy_1.78.2 DelayedArray_0.26.7
[34] limma_3.56.2 iterators_1.0.14 abind_1.4-5
[37] foreach_1.5.2 tidyselect_1.2.0 locfit_1.5-9.8
[40] digest_0.6.33 dplyr_1.1.3 labeling_0.4.3
[43] colorspace_2.1-0 cli_3.6.1 magrittr_2.0.3
[46] S4Arrays_1.0.6 utf8_1.2.3 withr_2.5.0
[49] scales_1.2.1 XVector_0.40.0 affyio_1.70.0
[52] GetoptLong_1.0.5 png_0.1-8 evaluate_0.21
[55] knitr_1.43 doParallel_1.0.17 rlang_1.1.1
[58] Rcpp_1.0.11 glue_1.6.2 BiocManager_1.30.22
[61] renv_1.0.2 R6_2.5.1 zlibbioc_1.46.0
```

:::::::::::::::::::::::::::::::::::::::: keypoints
Expand Down
8 changes: 4 additions & 4 deletions 07-gene-set-analysis.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -501,9 +501,9 @@ microbenchmark(

```{.output}
Unit: microseconds
expr min lq mean median uq max neval
fisher 281.3 286.50 298.429 291.2 303.3 530.4 100
hyper 1.6 1.85 2.576 2.3 2.6 18.5 100
expr min lq mean median uq max neval
fisher 321.3 328.6 345.094 335.25 349.55 689.0 100
hyper 1.7 2.3 3.487 3.25 4.30 27.2 100
```

It is very astonishing that `phyper()` is hundreds of times faster than
Expand Down Expand Up @@ -1231,7 +1231,7 @@ resTimeGO = enrichGO(gene = timeDEgenes,
```

```{.output}
--> Expected input gene ID: 19725,67042,103733,56484,23967,380709
--> Expected input gene ID: 20317,19156,226265,387218,15270,70235
```

```{.output}
Expand Down
86 changes: 0 additions & 86 deletions config.yaml
View file

This file was deleted.

Binary file modified fig/05-differential-expression-rendered-unnamed-chunk-19-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file removed fig/06-extra-design-rendered-unnamed-chunk-13-2.png
View file
Binary file not shown.
Binary file removed fig/06-extra-design-rendered-unnamed-chunk-18-2.png
View file
Binary file not shown.
Binary file removed fig/06-extra-design-rendered-unnamed-chunk-23-2.png
View file
Binary file not shown.
Binary file removed fig/06-extra-design-rendered-unnamed-chunk-26-2.png
View file
Binary file not shown.
Binary file modified fig/07-gene-set-analysis-rendered-unnamed-chunk-15-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
36 changes: 18 additions & 18 deletions md5sum.txt
View file
Original file line number Diff line number Diff line change
@@ -1,19 +1,19 @@
"file" "checksum" "built" "date"
"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-09-02"
"LICENSE.md" "2fb7308e51efc6894f5fb9794505973e" "site/built/LICENSE.md" "2023-09-02"
"config.yaml" "297622287fe4f84b2f8e1792cef52216" "site/built/config.yaml" "2023-09-02"
"index.md" "6a1b0b9e8983481699e2e4ef54a4893a" "site/built/index.md" "2023-09-02"
"episodes/01-intro-to-rnaseq.Rmd" "7cc3f4922347f6d5d9ef80dd31e84fbb" "site/built/01-intro-to-rnaseq.md" "2023-09-03"
"episodes/02-setup.Rmd" "045d2eb353af1b96f2c2517d101b0e83" "site/built/02-setup.md" "2023-09-02"
"episodes/03-import-annotate.Rmd" "d653abfd6c1d42cd9ec18fdce069750d" "site/built/03-import-annotate.md" "2023-09-03"
"episodes/04-exploratory-qc.Rmd" "021a9d1bf42604007437989c83cbe272" "site/built/04-exploratory-qc.md" "2023-09-02"
"episodes/05-differential-expression.Rmd" "b92c0136718c4323383f0a238b9dff5a" "site/built/05-differential-expression.md" "2023-09-03"
"episodes/06-extra-design.Rmd" "9e306e2946dd2c6def3dab47829d48f1" "site/built/06-extra-design.md" "2023-09-03"
"episodes/07-gene-set-analysis.Rmd" "5f4225021c67b8782959c311f74f651a" "site/built/07-gene-set-analysis.md" "2023-09-02"
"episodes/08-next-steps.Rmd" "88227f8b7b9ae91bd86a66a93d722946" "site/built/08-next-steps.md" "2023-09-02"
"instructors/instructor-notes.md" "a59fd3b94c07c3fe3218c054a0f03277" "site/built/instructor-notes.md" "2023-09-02"
"learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2023-09-02"
"learners/reference.md" "b9aea3dd8169bf1105bf4f462e8e38f5" "site/built/reference.md" "2023-09-02"
"learners/setup.md" "ffaa01a8e1cbf5ea0acf405ecd867e07" "site/built/setup.md" "2023-09-02"
"profiles/learner-profiles.md" "28ba7f4d04639862db131119f4dc4f4d" "site/built/learner-profiles.md" "2023-09-02"
"renv/profiles/lesson-requirements/renv.lock" "2726a60e3128302517dc78b3d3d870a3" "site/built/renv.lock" "2023-09-02"
"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-09-05"
"LICENSE.md" "2fb7308e51efc6894f5fb9794505973e" "site/built/LICENSE.md" "2023-09-05"
"config.yaml" "297622287fe4f84b2f8e1792cef52216" "site/built/config.yaml" "2023-09-05"
"index.md" "6a1b0b9e8983481699e2e4ef54a4893a" "site/built/index.md" "2023-09-05"
"episodes/01-intro-to-rnaseq.Rmd" "7cc3f4922347f6d5d9ef80dd31e84fbb" "site/built/01-intro-to-rnaseq.md" "2023-09-05"
"episodes/02-setup.Rmd" "045d2eb353af1b96f2c2517d101b0e83" "site/built/02-setup.md" "2023-09-05"
"episodes/03-import-annotate.Rmd" "d653abfd6c1d42cd9ec18fdce069750d" "site/built/03-import-annotate.md" "2023-09-05"
"episodes/04-exploratory-qc.Rmd" "021a9d1bf42604007437989c83cbe272" "site/built/04-exploratory-qc.md" "2023-09-05"
"episodes/05-differential-expression.Rmd" "b92c0136718c4323383f0a238b9dff5a" "site/built/05-differential-expression.md" "2023-09-05"
"episodes/06-extra-design.Rmd" "9e306e2946dd2c6def3dab47829d48f1" "site/built/06-extra-design.md" "2023-09-05"
"episodes/07-gene-set-analysis.Rmd" "5f4225021c67b8782959c311f74f651a" "site/built/07-gene-set-analysis.md" "2023-09-05"
"episodes/08-next-steps.Rmd" "88227f8b7b9ae91bd86a66a93d722946" "site/built/08-next-steps.md" "2023-09-05"
"instructors/instructor-notes.md" "a59fd3b94c07c3fe3218c054a0f03277" "site/built/instructor-notes.md" "2023-09-05"
"learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2023-09-05"
"learners/reference.md" "b9aea3dd8169bf1105bf4f462e8e38f5" "site/built/reference.md" "2023-09-05"
"learners/setup.md" "ffaa01a8e1cbf5ea0acf405ecd867e07" "site/built/setup.md" "2023-09-05"
"profiles/learner-profiles.md" "28ba7f4d04639862db131119f4dc4f4d" "site/built/learner-profiles.md" "2023-09-05"
"renv/profiles/lesson-requirements/renv.lock" "f4b76fd34da291a2582334fac2a0fa8d" "site/built/renv.lock" "2023-09-05"
Loading

0 comments on commit 3c789c8

Please sign in to comment.