diff --git a/03-import-annotate.md b/03-import-annotate.md index 61a8baeb..7f45fb55 100644 --- a/03-import-annotate.md +++ b/03-import-annotate.md @@ -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 ``` diff --git a/04-exploratory-qc.md b/04-exploratory-qc.md index 4303421e..1f5e85d7 100644 --- a/04-exploratory-qc.md +++ b/04-exploratory-qc.md @@ -427,7 +427,7 @@ 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 @@ -435,34 +435,34 @@ other attached packages: 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 ``` diff --git a/07-gene-set-analysis.md b/07-gene-set-analysis.md index bdfcccd3..e7215c4f 100644 --- a/07-gene-set-analysis.md +++ b/07-gene-set-analysis.md @@ -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 @@ -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} @@ -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 diff --git a/config.yaml b/config.yaml deleted file mode 100644 index 94b86364..00000000 --- a/config.yaml +++ /dev/null @@ -1,86 +0,0 @@ -#------------------------------------------------------------ -# Values for this lesson. -#------------------------------------------------------------ - -# Which carpentry is this (swc, dc, lc, or cp)? -# swc: Software Carpentry -# dc: Data Carpentry -# lc: Library Carpentry -# cp: Carpentries (to use for instructor training for instance) -# incubator: The Carpentries Incubator -carpentry: 'incubator' -varnish: mblue9/varnish - -# Overall title for pages. -title: 'RNA-seq analysis with Bioconductor' - -# Date the lesson was created (YYYY-MM-DD, this is empty by default) -created: '2020-09-15' - -# Comma-separated list of keywords for the lesson -keywords: 'software, data, lesson, The Carpentries' - -# Life cycle stage of the lesson -# possible values: pre-alpha, alpha, beta, stable -life_cycle: 'pre-alpha' - -# License of the lesson -license: 'CC-BY 4.0' - -# Link to the source repository for this lesson -source: 'https://github.com/carpentries-incubator/bioc-rnaseq' - -# Default branch of your lesson -branch: 'main' - -# Who to contact if there are any issues -contact: 'charlotte.soneson@fmi.ch' - -# Navigation ------------------------------------------------ -# -# Use the following menu items to specify the order of -# individual pages in each dropdown section. Leave blank to -# include all pages in the folder. -# -# Example ------------- -# -# episodes: -# - introduction.md -# - first-steps.md -# -# learners: -# - setup.md -# -# instructors: -# - instructor-notes.md -# -# profiles: -# - one-learner.md -# - another-learner.md - -# Order of episodes in your lesson -episodes: -- 01-intro-to-rnaseq.Rmd -- 02-setup.Rmd -- 03-import-annotate.Rmd -- 04-exploratory-qc.Rmd -- 05-differential-expression.Rmd -- 06-extra-design.Rmd -- 07-gene-set-analysis.Rmd -- 08-next-steps.Rmd - -# Information for Learners -learners: - -# Information for Instructors -instructors: - -# Learner Profiles -profiles: - -# Customisation --------------------------------------------- -# -# This space below is where custom yaml items (e.g. pinning -# sandpaper and varnish versions) should live - -url: https://carpentries-incubator.github.io/bioc-rnaseq diff --git a/fig/04-exploratory-qc-rendered-pca-exercise-1.png b/fig/04-exploratory-qc-rendered-pca-exercise-1.png index 3a80b3f2..25e565b8 100644 Binary files a/fig/04-exploratory-qc-rendered-pca-exercise-1.png and b/fig/04-exploratory-qc-rendered-pca-exercise-1.png differ diff --git a/fig/05-differential-expression-rendered-heatmap-time-1.png b/fig/05-differential-expression-rendered-heatmap-time-1.png index fcae0d16..7a365516 100644 Binary files a/fig/05-differential-expression-rendered-heatmap-time-1.png and b/fig/05-differential-expression-rendered-heatmap-time-1.png differ diff --git a/fig/07-gene-set-analysis-rendered-hypergeom-1.png b/fig/07-gene-set-analysis-rendered-hypergeom-1.png index 950e15f0..a02c0f23 100644 Binary files a/fig/07-gene-set-analysis-rendered-hypergeom-1.png and b/fig/07-gene-set-analysis-rendered-hypergeom-1.png differ diff --git a/md5sum.txt b/md5sum.txt index ac09f717..ab785f89 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -1,19 +1,19 @@ "file" "checksum" "built" "date" -"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2023-11-21" -"LICENSE.md" "2fb7308e51efc6894f5fb9794505973e" "site/built/LICENSE.md" "2023-11-21" -"config.yaml" "297622287fe4f84b2f8e1792cef52216" "site/built/config.yaml" "2023-11-21" -"index.md" "6a1b0b9e8983481699e2e4ef54a4893a" "site/built/index.md" "2023-11-21" -"episodes/01-intro-to-rnaseq.Rmd" "b4d2d36be5042834578061b30665d493" "site/built/01-intro-to-rnaseq.md" "2023-11-21" -"episodes/02-setup.Rmd" "e62af0b59eec704194484af83db5b859" "site/built/02-setup.md" "2023-11-21" -"episodes/03-import-annotate.Rmd" "c43d8eab0fcc982993ea35a952d323c0" "site/built/03-import-annotate.md" "2023-11-21" -"episodes/04-exploratory-qc.Rmd" "af033b6158f06de3f33d41673272a87d" "site/built/04-exploratory-qc.md" "2023-11-21" -"episodes/05-differential-expression.Rmd" "29ab3939367a0b3521cfd764929e3aee" "site/built/05-differential-expression.md" "2023-11-21" -"episodes/06-extra-design.Rmd" "e4859b8e76bc6d0c8d5c598e1d00b37b" "site/built/06-extra-design.md" "2023-11-21" -"episodes/07-gene-set-analysis.Rmd" "e7b69b6f2af11dfab883303e9a50981d" "site/built/07-gene-set-analysis.md" "2023-11-21" -"episodes/08-next-steps.Rmd" "88227f8b7b9ae91bd86a66a93d722946" "site/built/08-next-steps.md" "2023-11-21" -"instructors/instructor-notes.md" "a59fd3b94c07c3fe3218c054a0f03277" "site/built/instructor-notes.md" "2023-11-21" -"learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2023-11-21" -"learners/reference.md" "b9aea3dd8169bf1105bf4f462e8e38f5" "site/built/reference.md" "2023-11-21" -"learners/setup.md" "29d12719c4fcebc031f726275706b330" "site/built/setup.md" "2023-11-21" -"profiles/learner-profiles.md" "28ba7f4d04639862db131119f4dc4f4d" "site/built/learner-profiles.md" "2023-11-21" -"renv/profiles/lesson-requirements/renv.lock" "3df0212a6f04d1ff01df5e98dc4fca51" "site/built/renv.lock" "2023-11-21" +"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-01-02" +"LICENSE.md" "2fb7308e51efc6894f5fb9794505973e" "site/built/LICENSE.md" "2024-01-02" +"config.yaml" "297622287fe4f84b2f8e1792cef52216" "site/built/config.yaml" "2024-01-02" +"index.md" "6a1b0b9e8983481699e2e4ef54a4893a" "site/built/index.md" "2024-01-02" +"episodes/01-intro-to-rnaseq.Rmd" "b4d2d36be5042834578061b30665d493" "site/built/01-intro-to-rnaseq.md" "2024-01-02" +"episodes/02-setup.Rmd" "e62af0b59eec704194484af83db5b859" "site/built/02-setup.md" "2024-01-02" +"episodes/03-import-annotate.Rmd" "c43d8eab0fcc982993ea35a952d323c0" "site/built/03-import-annotate.md" "2024-01-02" +"episodes/04-exploratory-qc.Rmd" "af033b6158f06de3f33d41673272a87d" "site/built/04-exploratory-qc.md" "2024-01-02" +"episodes/05-differential-expression.Rmd" "29ab3939367a0b3521cfd764929e3aee" "site/built/05-differential-expression.md" "2024-01-02" +"episodes/06-extra-design.Rmd" "e4859b8e76bc6d0c8d5c598e1d00b37b" "site/built/06-extra-design.md" "2024-01-02" +"episodes/07-gene-set-analysis.Rmd" "e7b69b6f2af11dfab883303e9a50981d" "site/built/07-gene-set-analysis.md" "2024-01-02" +"episodes/08-next-steps.Rmd" "88227f8b7b9ae91bd86a66a93d722946" "site/built/08-next-steps.md" "2024-01-02" +"instructors/instructor-notes.md" "a59fd3b94c07c3fe3218c054a0f03277" "site/built/instructor-notes.md" "2024-01-02" +"learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2024-01-02" +"learners/reference.md" "b9aea3dd8169bf1105bf4f462e8e38f5" "site/built/reference.md" "2024-01-02" +"learners/setup.md" "29d12719c4fcebc031f726275706b330" "site/built/setup.md" "2024-01-02" +"profiles/learner-profiles.md" "28ba7f4d04639862db131119f4dc4f4d" "site/built/learner-profiles.md" "2024-01-02" +"renv/profiles/lesson-requirements/renv.lock" "4d9bb6b02b1076a6e8ade8bb240dae24" "site/built/renv.lock" "2024-01-02" diff --git a/renv.lock b/renv.lock deleted file mode 100644 index 0afcd44d..00000000 --- a/renv.lock +++ /dev/null @@ -1,2923 +0,0 @@ -{ - "R": { - "Version": "4.3.2", - "Repositories": [ - { - "Name": "BioCsoft", - "URL": "https://bioconductor.org/packages/3.17/bioc" - }, - { - "Name": "BioCann", - "URL": "https://bioconductor.org/packages/3.17/data/annotation" - }, - { - "Name": "BioCexp", - "URL": "https://bioconductor.org/packages/3.17/data/experiment" - }, - { - "Name": "BioCworkflows", - "URL": "https://bioconductor.org/packages/3.17/workflows" - }, - { - "Name": "BioCbooks", - "URL": "https://bioconductor.org/packages/3.17/books" - }, - { - "Name": "carpentries", - "URL": "https://carpentries.r-universe.dev" - }, - { - "Name": "carpentries_archive", - "URL": "https://carpentries.github.io/drat" - }, - { - "Name": "CRAN", - "URL": "https://cran.rstudio.com" - } - ] - }, - "Bioconductor": { - "Version": "3.17" - }, - "Packages": { - "AnnotationDbi": { - "Package": "AnnotationDbi", - "Version": "1.62.2", - "Source": "Bioconductor", - "Requirements": [ - "Biobase", - "BiocGenerics", - "DBI", - "IRanges", - "KEGGREST", - "R", - "RSQLite", - "S4Vectors", - "methods", - "stats", - "stats4" - ], - "Hash": "e6c671413b55490c11402f78889384d9" - }, - "BH": { - "Package": "BH", - "Version": "1.81.0-1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "68122010f01c4dcfbe58ce7112f2433d" - }, - "Biobase": { - "Package": "Biobase", - "Version": "2.60.0", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "R", - "methods", - "utils" - ], - "Hash": "ed269b250f5844d54dfdc7e749f901aa" - }, - "BiocGenerics": { - "Package": "BiocGenerics", - "Version": "0.46.0", - "Source": "Bioconductor", - "Requirements": [ - "R", - "graphics", - "methods", - "stats", - "utils" - ], - "Hash": "c179ae59955c36f5d0068ed29ce832f7" - }, - "BiocManager": { - "Package": "BiocManager", - "Version": "1.30.22", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "d57e43105a1aa9cb54fdb4629725acb1" - }, - "BiocParallel": { - "Package": "BiocParallel", - "Version": "1.34.2", - "Source": "Bioconductor", - "Requirements": [ - "BH", - "R", - "codetools", - "cpp11", - "futile.logger", - "methods", - "parallel", - "snow", - "stats", - "utils" - ], - "Hash": "84347b6a8118ba2182b148298b118f0e" - }, - "BiocVersion": { - "Package": "BiocVersion", - "Version": "3.17.1", - "Source": "Bioconductor", - "Requirements": [ - "R" - ], - "Hash": "f7c0d5521799b7b0d0a211143ed0bfcb" - }, - "Biostrings": { - "Package": "Biostrings", - "Version": "2.68.1", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "GenomeInfoDb", - "IRanges", - "R", - "S4Vectors", - "XVector", - "crayon", - "grDevices", - "graphics", - "methods", - "stats", - "utils" - ], - "Hash": "838eef43ab267a7409d68ba0fa8da5fa" - }, - "ComplexHeatmap": { - "Package": "ComplexHeatmap", - "Version": "2.16.0", - "Source": "Bioconductor", - "Requirements": [ - "GetoptLong", - "GlobalOptions", - "IRanges", - "R", - "RColorBrewer", - "circlize", - "clue", - "codetools", - "colorspace", - "digest", - "doParallel", - "foreach", - "grDevices", - "graphics", - "grid", - "matrixStats", - "methods", - "png", - "stats" - ], - "Hash": "e40659423f418fdb232649155f3cfac1" - }, - "DBI": { - "Package": "DBI", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "b2866e62bab9378c3cc9476a1954226b" - }, - "DESeq2": { - "Package": "DESeq2", - "Version": "1.40.2", - "Source": "Bioconductor", - "Requirements": [ - "Biobase", - "BiocGenerics", - "BiocParallel", - "GenomicRanges", - "IRanges", - "Rcpp", - "RcppArmadillo", - "S4Vectors", - "SummarizedExperiment", - "ggplot2", - "locfit", - "matrixStats", - "methods", - "stats4" - ], - "Hash": "867008cb7070cf00bb5912218f8600e3" - }, - "DOSE": { - "Package": "DOSE", - "Version": "3.26.2", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "BiocParallel", - "GOSemSim", - "HDO.db", - "R", - "fgsea", - "ggplot2", - "methods", - "qvalue", - "reshape2", - "stats", - "utils" - ], - "Hash": "d33bf9add091a5f7bb152809af75be9c" - }, - "DT": { - "Package": "DT", - "Version": "0.30", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "crosstalk", - "htmltools", - "htmlwidgets", - "httpuv", - "jquerylib", - "jsonlite", - "magrittr", - "promises" - ], - "Hash": "dffb4d94a00be1b4a4507e53ab95bd90" - }, - "DelayedArray": { - "Package": "DelayedArray", - "Version": "0.26.7", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "IRanges", - "Matrix", - "MatrixGenerics", - "R", - "S4Arrays", - "S4Vectors", - "methods", - "stats", - "stats4" - ], - "Hash": "ef6ff3e15ce624118e6cf8151e58e38c" - }, - "ExploreModelMatrix": { - "Package": "ExploreModelMatrix", - "Version": "1.12.0", - "Source": "Bioconductor", - "Requirements": [ - "DT", - "MASS", - "S4Vectors", - "cowplot", - "dplyr", - "ggplot2", - "limma", - "magrittr", - "methods", - "rintrojs", - "scales", - "shiny", - "shinydashboard", - "shinyjs", - "stats", - "tibble", - "tidyr", - "utils" - ], - "Hash": "f460a3a7d68926b1b102c1f2f1472656" - }, - "GO.db": { - "Package": "GO.db", - "Version": "3.17.0", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "R", - "methods" - ], - "Hash": "9b2c8cc59a6eb89b20deed9f4c4a9870" - }, - "GOSemSim": { - "Package": "GOSemSim", - "Version": "2.26.1", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "GO.db", - "R", - "Rcpp", - "methods", - "utils" - ], - "Hash": "b27837cc8c91273e45563693f1017221" - }, - "GenomeInfoDb": { - "Package": "GenomeInfoDb", - "Version": "1.36.4", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "GenomeInfoDbData", - "IRanges", - "R", - "RCurl", - "S4Vectors", - "methods", - "stats", - "stats4", - "utils" - ], - "Hash": "1c6756527d78e8135d34662d2e1d54ec" - }, - "GenomeInfoDbData": { - "Package": "GenomeInfoDbData", - "Version": "1.2.10", - "Source": "Bioconductor", - "Requirements": [ - "R" - ], - "Hash": "56294b21068b8cb5db1c47d0a42f307b" - }, - "GenomicRanges": { - "Package": "GenomicRanges", - "Version": "1.52.1", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "GenomeInfoDb", - "IRanges", - "R", - "S4Vectors", - "XVector", - "methods", - "stats", - "stats4", - "utils" - ], - "Hash": "c9471497a07953ded9b8889879c079e9" - }, - "GetoptLong": { - "Package": "GetoptLong", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "GlobalOptions", - "R", - "crayon", - "methods", - "rjson" - ], - "Hash": "61fac01c73abf03ac72e88dc3952c1e3" - }, - "GlobalOptions": { - "Package": "GlobalOptions", - "Version": "0.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods", - "utils" - ], - "Hash": "c3f7b221e60c28f5f3533d74c6fef024" - }, - "HDO.db": { - "Package": "HDO.db", - "Version": "0.99.1", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "R", - "methods", - "utils" - ], - "Hash": "be08478e9424bbb54a3890d08e01192b" - }, - "IRanges": { - "Package": "IRanges", - "Version": "2.34.1", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "R", - "S4Vectors", - "methods", - "stats", - "stats4", - "utils" - ], - "Hash": "18939552437a335b59fb381e508275d6" - }, - "KEGGREST": { - "Package": "KEGGREST", - "Version": "1.40.1", - "Source": "Bioconductor", - "Requirements": [ - "Biostrings", - "R", - "httr", - "methods", - "png" - ], - "Hash": "2988b310648d92e9d5c877d627068b9d" - }, - "KernSmooth": { - "Package": "KernSmooth", - "Version": "2.23-22", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats" - ], - "Hash": "2fecebc3047322fa5930f74fae5de70f" - }, - "MASS": { - "Package": "MASS", - "Version": "7.3-60", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "methods", - "stats", - "utils" - ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" - }, - "Matrix": { - "Package": "Matrix", - "Version": "1.6-1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "grid", - "lattice", - "methods", - "stats", - "utils" - ], - "Hash": "1a00d4828f33a9d690806e98bd17150c" - }, - "MatrixGenerics": { - "Package": "MatrixGenerics", - "Version": "1.12.3", - "Source": "Bioconductor", - "Requirements": [ - "matrixStats", - "methods" - ], - "Hash": "10a6bd0dcabaeede87616e4465b6ac6f" - }, - "R6": { - "Package": "R6", - "Version": "2.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" - }, - "RColorBrewer": { - "Package": "RColorBrewer", - "Version": "1.1-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "45f0398006e83a5b10b72a90663d8d8c" - }, - "RCurl": { - "Package": "RCurl", - "Version": "1.98-1.13", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bitops", - "methods" - ], - "Hash": "318c7b8d68358b45cbc6115dda23d7db" - }, - "RSQLite": { - "Package": "RSQLite", - "Version": "2.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "DBI", - "R", - "bit64", - "blob", - "cpp11", - "memoise", - "methods", - "pkgconfig", - "plogr" - ], - "Hash": "3de9b130745b42015c060758cf6d9b8d" - }, - "Rcpp": { - "Package": "Rcpp", - "Version": "1.0.11", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods", - "utils" - ], - "Hash": "ae6cbbe1492f4de79c45fce06f967ce8" - }, - "RcppArmadillo": { - "Package": "RcppArmadillo", - "Version": "0.12.6.6.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "methods", - "stats", - "utils" - ], - "Hash": "aabc6cb0f0953d0442d3c82d8a9d2610" - }, - "RcppEigen": { - "Package": "RcppEigen", - "Version": "0.3.3.9.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "stats", - "utils" - ], - "Hash": "acb0a5bf38490f26ab8661b467f4f53a" - }, - "RcppNumerical": { - "Package": "RcppNumerical", - "Version": "0.6-0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Rcpp", - "RcppEigen" - ], - "Hash": "a008f094e60e88cef2472ef0e057f90e" - }, - "S4Arrays": { - "Package": "S4Arrays", - "Version": "1.0.6", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "IRanges", - "Matrix", - "R", - "S4Vectors", - "abind", - "crayon", - "methods", - "stats" - ], - "Hash": "2b40d107b4a6fbd3f0cc81214d0b2891" - }, - "S4Vectors": { - "Package": "S4Vectors", - "Version": "0.38.2", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "R", - "methods", - "stats", - "stats4", - "utils" - ], - "Hash": "338207894998073e7823706f886a1386" - }, - "SingleCellExperiment": { - "Package": "SingleCellExperiment", - "Version": "1.22.0", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "DelayedArray", - "GenomicRanges", - "S4Vectors", - "SummarizedExperiment", - "methods", - "stats", - "utils" - ], - "Hash": "47569baf7560bf8e3ba57386e9672f7f" - }, - "SummarizedExperiment": { - "Package": "SummarizedExperiment", - "Version": "1.30.2", - "Source": "Bioconductor", - "Requirements": [ - "Biobase", - "BiocGenerics", - "DelayedArray", - "GenomeInfoDb", - "GenomicRanges", - "IRanges", - "Matrix", - "MatrixGenerics", - "R", - "S4Arrays", - "S4Vectors", - "methods", - "stats", - "tools", - "utils" - ], - "Hash": "6af56fbcb57deb9b094a352beee9a202" - }, - "XVector": { - "Package": "XVector", - "Version": "0.40.0", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "IRanges", - "R", - "S4Vectors", - "methods", - "tools", - "utils", - "zlibbioc" - ], - "Hash": "cc3048ef590a16ff55a5e3149d5e060b" - }, - "abind": { - "Package": "abind", - "Version": "1.4-5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods", - "utils" - ], - "Hash": "4f57884290cc75ab22f4af9e9d4ca862" - }, - "affy": { - "Package": "affy", - "Version": "1.78.2", - "Source": "Bioconductor", - "Requirements": [ - "Biobase", - "BiocGenerics", - "BiocManager", - "R", - "affyio", - "grDevices", - "graphics", - "methods", - "preprocessCore", - "stats", - "utils", - "zlibbioc" - ], - "Hash": "8dc58f7e9086da714fbfcaf100b95304" - }, - "affyio": { - "Package": "affyio", - "Version": "1.70.0", - "Source": "Bioconductor", - "Requirements": [ - "R", - "methods", - "zlibbioc" - ], - "Hash": "283c9a759c6592e2fdac1f7b83ab9442" - }, - "anytime": { - "Package": "anytime", - "Version": "0.3.9", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "BH", - "R", - "Rcpp" - ], - "Hash": "74a64813f17b492da9c6afda6b128e3d" - }, - "ape": { - "Package": "ape", - "Version": "5.7-1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "digest", - "graphics", - "lattice", - "methods", - "nlme", - "parallel", - "stats", - "utils" - ], - "Hash": "10705eec964349f270504754d8fe8ef1" - }, - "apeglm": { - "Package": "apeglm", - "Version": "1.22.1", - "Source": "Bioconductor", - "Requirements": [ - "GenomicRanges", - "Rcpp", - "RcppEigen", - "RcppNumerical", - "SummarizedExperiment", - "emdbook", - "methods", - "stats", - "utils" - ], - "Hash": "7aa41e1a8217e28969c58d82a5477512" - }, - "aplot": { - "Package": "aplot", - "Version": "0.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggfun", - "ggplot2", - "ggplotify", - "magrittr", - "methods", - "patchwork", - "utils" - ], - "Hash": "869a35e6d38fe9936eb578e09091842b" - }, - "askpass": { - "Package": "askpass", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "sys" - ], - "Hash": "cad6cf7f1d5f6e906700b9d3e718c796" - }, - "babelgene": { - "Package": "babelgene", - "Version": "22.9", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "dplyr", - "methods", - "rlang" - ], - "Hash": "8288e81d0c2c3272603f6ef394ffa6fd" - }, - "base64enc": { - "Package": "base64enc", - "Version": "0.1-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "543776ae6848fde2f48ff3816d0628bc" - }, - "bbmle": { - "Package": "bbmle", - "Version": "1.0.25", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "MASS", - "Matrix", - "R", - "bdsmatrix", - "lattice", - "methods", - "mvtnorm", - "numDeriv", - "stats", - "stats4" - ], - "Hash": "ded471b3be03b4c65419abbc1b5e9f86" - }, - "bdsmatrix": { - "Package": "bdsmatrix", - "Version": "1.3-6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "b55d57db210e5af3f097ae228aadaf50" - }, - "bit": { - "Package": "bit", - "Version": "4.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "d242abec29412ce988848d0294b208fd" - }, - "bit64": { - "Package": "bit64", - "Version": "4.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bit", - "methods", - "stats", - "utils" - ], - "Hash": "9fe98599ca456d6552421db0d6772d8f" - }, - "bitops": { - "Package": "bitops", - "Version": "1.0-7", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "b7d8d8ee39869c18d8846a184dd8a1af" - }, - "blob": { - "Package": "blob", - "Version": "1.2.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods", - "rlang", - "vctrs" - ], - "Hash": "40415719b5a479b87949f3aa0aee737c" - }, - "bslib": { - "Package": "bslib", - "Version": "0.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "base64enc", - "cachem", - "grDevices", - "htmltools", - "jquerylib", - "jsonlite", - "memoise", - "mime", - "rlang", - "sass" - ], - "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9" - }, - "caTools": { - "Package": "caTools", - "Version": "1.18.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bitops" - ], - "Hash": "34d90fa5845004236b9eacafc51d07b2" - }, - "cachem": { - "Package": "cachem", - "Version": "1.0.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "fastmap", - "rlang" - ], - "Hash": "c35768291560ce302c0a6589f92e837d" - }, - "circlize": { - "Package": "circlize", - "Version": "0.4.15", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "GlobalOptions", - "R", - "colorspace", - "grDevices", - "graphics", - "grid", - "methods", - "shape", - "stats", - "utils" - ], - "Hash": "2bb47a2fe6ab009b1dcc5566d8c3a988" - }, - "cli": { - "Package": "cli", - "Version": "3.6.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "89e6d8219950eac806ae0c489052048a" - }, - "clue": { - "Package": "clue", - "Version": "0.3-65", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cluster", - "graphics", - "methods", - "stats" - ], - "Hash": "d6b53853800595408a776900bcc0c23f" - }, - "cluster": { - "Package": "cluster", - "Version": "2.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "stats", - "utils" - ], - "Hash": "5edbbabab6ce0bf7900a74fd4358628e" - }, - "clusterProfiler": { - "Package": "clusterProfiler", - "Version": "4.8.3", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "DOSE", - "GO.db", - "GOSemSim", - "R", - "downloader", - "dplyr", - "enrichplot", - "gson", - "magrittr", - "methods", - "plyr", - "qvalue", - "rlang", - "stats", - "tidyr", - "utils", - "yulab.utils" - ], - "Hash": "358573de6d0ae89b2a9c27bb1f061898" - }, - "coda": { - "Package": "coda", - "Version": "0.19-4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "lattice" - ], - "Hash": "24b6d006b8b2343876cf230687546932" - }, - "codetools": { - "Package": "codetools", - "Version": "0.2-19", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "c089a619a7fae175d149d89164f8c7d8" - }, - "colorspace": { - "Package": "colorspace", - "Version": "2.1-0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "methods", - "stats" - ], - "Hash": "f20c47fd52fae58b4e377c37bb8c335b" - }, - "colourpicker": { - "Package": "colourpicker", - "Version": "1.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", - "htmltools", - "htmlwidgets", - "jsonlite", - "miniUI", - "shiny", - "shinyjs", - "utils" - ], - "Hash": "daec8f7d4ba89df06fe2c0802c3a9dac" - }, - "commonmark": { - "Package": "commonmark", - "Version": "1.9.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "d691c61bff84bd63c383874d2d0c3307" - }, - "cowplot": { - "Package": "cowplot", - "Version": "1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", - "grDevices", - "grid", - "gtable", - "methods", - "rlang", - "scales" - ], - "Hash": "b418e8423699d11c7f2087c2bfd07da2" - }, - "cpp11": { - "Package": "cpp11", - "Version": "0.4.6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "707fae4bbf73697ec8d85f9d7076c061" - }, - "crayon": { - "Package": "crayon", - "Version": "1.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "methods", - "utils" - ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" - }, - "crosstalk": { - "Package": "crosstalk", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "htmltools", - "jsonlite", - "lazyeval" - ], - "Hash": "6aa54f69598c32177e920eb3402e8293" - }, - "curl": { - "Package": "curl", - "Version": "5.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "9123f3ef96a2c1a93927d828b2fe7d4c" - }, - "data.table": { - "Package": "data.table", - "Version": "1.14.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "b4c06e554f33344e044ccd7fdca750a9" - }, - "digest": { - "Package": "digest", - "Version": "0.6.33", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d" - }, - "doParallel": { - "Package": "doParallel", - "Version": "1.0.17", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "foreach", - "iterators", - "parallel", - "utils" - ], - "Hash": "451e5edf411987991ab6a5410c45011f" - }, - "downloader": { - "Package": "downloader", - "Version": "0.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "digest", - "utils" - ], - "Hash": "f4f2a915e0dedbdf016a83b63477349f" - }, - "dplyr": { - "Package": "dplyr", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "R", - "R6", - "cli", - "generics", - "glue", - "lifecycle", - "magrittr", - "methods", - "pillar", - "rlang", - "tibble", - "tidyselect", - "utils", - "vctrs" - ], - "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949" - }, - "ellipsis": { - "Package": "ellipsis", - "Version": "0.3.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "rlang" - ], - "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077" - }, - "emdbook": { - "Package": "emdbook", - "Version": "1.3.13", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "MASS", - "bbmle", - "coda", - "lattice", - "plyr" - ], - "Hash": "ed650db9168aeca46d35aa373b12e056" - }, - "enrichplot": { - "Package": "enrichplot", - "Version": "1.20.3", - "Source": "Bioconductor", - "Requirements": [ - "DOSE", - "GOSemSim", - "R", - "RColorBrewer", - "aplot", - "ggfun", - "ggnewscale", - "ggplot2", - "ggraph", - "ggtree", - "graphics", - "grid", - "igraph", - "magrittr", - "methods", - "plyr", - "purrr", - "reshape2", - "rlang", - "scatterpie", - "shadowtext", - "stats", - "utils", - "yulab.utils" - ], - "Hash": "e3706da8c0221f8592e80699c8a62a5d" - }, - "evaluate": { - "Package": "evaluate", - "Version": "0.23", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "daf4a1246be12c1fa8c7705a0935c1a0" - }, - "fansi": { - "Package": "fansi", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "utils" - ], - "Hash": "3e8583a60163b4bc1a80016e63b9959e" - }, - "farver": { - "Package": "farver", - "Version": "2.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "8106d78941f34855c440ddb946b8f7a5" - }, - "fastmap": { - "Package": "fastmap", - "Version": "1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "f7736a18de97dea803bde0a2daaafb27" - }, - "fastmatch": { - "Package": "fastmatch", - "Version": "1.1-4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "8c406b7284bbaef08e01c6687367f195" - }, - "fgsea": { - "Package": "fgsea", - "Version": "1.26.0", - "Source": "Bioconductor", - "Requirements": [ - "BH", - "BiocParallel", - "Matrix", - "R", - "Rcpp", - "cowplot", - "data.table", - "fastmatch", - "ggplot2", - "grid", - "scales", - "stats", - "utils" - ], - "Hash": "62342298a29521147ea0764b22e8121e" - }, - "fontawesome": { - "Package": "fontawesome", - "Version": "0.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "htmltools", - "rlang" - ], - "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" - }, - "foreach": { - "Package": "foreach", - "Version": "1.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "codetools", - "iterators", - "utils" - ], - "Hash": "618609b42c9406731ead03adf5379850" - }, - "formatR": { - "Package": "formatR", - "Version": "1.14", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "63cb26d12517c7863f5abb006c5e0f25" - }, - "fs": { - "Package": "fs", - "Version": "1.6.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "47b5f30c720c23999b913a1a635cf0bb" - }, - "futile.logger": { - "Package": "futile.logger", - "Version": "1.4.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "futile.options", - "lambda.r", - "utils" - ], - "Hash": "99f0ace8c05ec7d3683d27083c4f1e7e" - }, - "futile.options": { - "Package": "futile.options", - "Version": "1.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "0d9bf02413ddc2bbe8da9ce369dcdd2b" - }, - "generics": { - "Package": "generics", - "Version": "0.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "15e9634c0fcd294799e9b2e929ed1b86" - }, - "ggforce": { - "Package": "ggforce", - "Version": "0.4.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "MASS", - "R", - "Rcpp", - "RcppEigen", - "cli", - "ggplot2", - "grDevices", - "grid", - "gtable", - "lifecycle", - "polyclip", - "rlang", - "scales", - "stats", - "systemfonts", - "tidyselect", - "tweenr", - "utils", - "vctrs", - "withr" - ], - "Hash": "a06503f54e227f79b45a72df2946a2d2" - }, - "ggfun": { - "Package": "ggfun", - "Version": "0.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "ggplot2", - "grid", - "rlang", - "utils" - ], - "Hash": "4657d320971a330ecffd0e1260f58214" - }, - "ggnewscale": { - "Package": "ggnewscale", - "Version": "0.4.9", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "ggplot2" - ], - "Hash": "2d3ce9ca9737ecf195794c63fc40b990" - }, - "ggplot2": { - "Package": "ggplot2", - "Version": "3.4.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "MASS", - "R", - "cli", - "glue", - "grDevices", - "grid", - "gtable", - "isoband", - "lifecycle", - "mgcv", - "rlang", - "scales", - "stats", - "tibble", - "vctrs", - "withr" - ], - "Hash": "313d31eff2274ecf4c1d3581db7241f9" - }, - "ggplotify": { - "Package": "ggplotify", - "Version": "0.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", - "grDevices", - "graphics", - "grid", - "gridGraphics", - "yulab.utils" - ], - "Hash": "1547863db3b472cf7181973acf649f1a" - }, - "ggraph": { - "Package": "ggraph", - "Version": "2.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "MASS", - "R", - "Rcpp", - "cli", - "digest", - "dplyr", - "ggforce", - "ggplot2", - "ggrepel", - "graphlayouts", - "grid", - "gtable", - "igraph", - "lifecycle", - "rlang", - "scales", - "stats", - "tidygraph", - "utils", - "vctrs", - "viridis", - "withr" - ], - "Hash": "62672fd99df5df5814f442e9cd5ec29b" - }, - "ggrepel": { - "Package": "ggrepel", - "Version": "0.9.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "ggplot2", - "grid", - "rlang", - "scales", - "withr" - ], - "Hash": "e9839af82cc43fda486a638b68b439b2" - }, - "ggtree": { - "Package": "ggtree", - "Version": "3.8.2", - "Source": "Bioconductor", - "Requirements": [ - "R", - "ape", - "aplot", - "cli", - "dplyr", - "ggfun", - "ggplot2", - "grid", - "magrittr", - "methods", - "purrr", - "rlang", - "scales", - "stats", - "tidyr", - "tidytree", - "treeio", - "utils", - "yulab.utils" - ], - "Hash": "8959d04f88a175de3f0cd2b46b4c2a65" - }, - "glue": { - "Package": "glue", - "Version": "1.6.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "methods" - ], - "Hash": "4f2596dfb05dac67b9dc558e5c6fba2e" - }, - "gplots": { - "Package": "gplots", - "Version": "3.1.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "KernSmooth", - "R", - "caTools", - "gtools", - "methods", - "stats" - ], - "Hash": "75437dd4c43599f6e9418ea249495fda" - }, - "graphlayouts": { - "Package": "graphlayouts", - "Version": "1.0.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "RcppArmadillo", - "igraph" - ], - "Hash": "468c98df6feea8aacf159eee906e7ee8" - }, - "gridExtra": { - "Package": "gridExtra", - "Version": "2.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "graphics", - "grid", - "gtable", - "utils" - ], - "Hash": "7d7f283939f563670a697165b2cf5560" - }, - "gridGraphics": { - "Package": "gridGraphics", - "Version": "0.5-1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "graphics", - "grid" - ], - "Hash": "5b79228594f02385d4df4979284879ae" - }, - "gson": { - "Package": "gson", - "Version": "0.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "jsonlite", - "methods", - "rlang", - "stats", - "tidyr", - "utils" - ], - "Hash": "d37d82cf043b679dd802e91d0b2ef6a1" - }, - "gtable": { - "Package": "gtable", - "Version": "0.3.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "grid", - "lifecycle", - "rlang" - ], - "Hash": "b29cf3031f49b04ab9c852c912547eef" - }, - "gtools": { - "Package": "gtools", - "Version": "3.9.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods", - "stats", - "utils" - ], - "Hash": "88bb96eaf7140cdf29e374ef74182220" - }, - "hexbin": { - "Package": "hexbin", - "Version": "1.28.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "grid", - "lattice", - "methods", - "stats", - "utils" - ], - "Hash": "124e384c01d8746f1c12f9dc1b80a161" - }, - "hgu95av2.db": { - "Package": "hgu95av2.db", - "Version": "3.13.0", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "R", - "methods", - "org.Hs.eg.db" - ], - "Hash": "aa0e0c100541f56ff41936077402c27c" - }, - "highr": { - "Package": "highr", - "Version": "0.10", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "xfun" - ], - "Hash": "06230136b2d2b9ba5805e1963fa6e890" - }, - "htmltools": { - "Package": "htmltools", - "Version": "0.5.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "base64enc", - "digest", - "ellipsis", - "fastmap", - "grDevices", - "rlang", - "utils" - ], - "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" - }, - "htmlwidgets": { - "Package": "htmlwidgets", - "Version": "1.6.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grDevices", - "htmltools", - "jsonlite", - "knitr", - "rmarkdown", - "yaml" - ], - "Hash": "a865aa85bcb2697f47505bfd70422471" - }, - "httpuv": { - "Package": "httpuv", - "Version": "1.6.12", - "Source": "Repository", - "Repository": "https://carpentries.r-universe.dev", - "Requirements": [ - "R", - "R6", - "Rcpp", - "later", - "promises", - "utils" - ], - "Hash": "c992f75861325961c29a188b45e549f7" - }, - "httr": { - "Package": "httr", - "Version": "1.4.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "curl", - "jsonlite", - "mime", - "openssl" - ], - "Hash": "ac107251d9d9fd72f0ca8049988f1d7f" - }, - "iSEE": { - "Package": "iSEE", - "Version": "2.12.0", - "Source": "Bioconductor", - "Requirements": [ - "BiocGenerics", - "ComplexHeatmap", - "DT", - "S4Vectors", - "SingleCellExperiment", - "SummarizedExperiment", - "circlize", - "colourpicker", - "ggplot2", - "ggrepel", - "grDevices", - "graphics", - "grid", - "igraph", - "methods", - "mgcv", - "rintrojs", - "shiny", - "shinyAce", - "shinyWidgets", - "shinydashboard", - "shinyjs", - "stats", - "utils", - "vipor", - "viridisLite" - ], - "Hash": "d7fca086ca345b01e2f313222e9d7f23" - }, - "igraph": { - "Package": "igraph", - "Version": "1.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Matrix", - "R", - "cli", - "cpp11", - "grDevices", - "graphics", - "lifecycle", - "magrittr", - "methods", - "pkgconfig", - "rlang", - "stats", - "utils" - ], - "Hash": "80401cb5ec513e8ddc56764d03f63669" - }, - "isoband": { - "Package": "isoband", - "Version": "0.2.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "grid", - "utils" - ], - "Hash": "0080607b4a1a7b28979aecef976d8bc2" - }, - "iterators": { - "Package": "iterators", - "Version": "1.0.14", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "8954069286b4b2b0d023d1b288dce978" - }, - "jquerylib": { - "Package": "jquerylib", - "Version": "0.1.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "htmltools" - ], - "Hash": "5aab57a3bd297eee1c1d862735972182" - }, - "jsonlite": { - "Package": "jsonlite", - "Version": "1.8.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "methods" - ], - "Hash": "266a20443ca13c65688b2116d5220f76" - }, - "knitr": { - "Package": "knitr", - "Version": "1.45", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "evaluate", - "highr", - "methods", - "tools", - "xfun", - "yaml" - ], - "Hash": "1ec462871063897135c1bcbe0fc8f07d" - }, - "labeling": { - "Package": "labeling", - "Version": "0.4.3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "graphics", - "stats" - ], - "Hash": "b64ec208ac5bc1852b285f665d6368b3" - }, - "lambda.r": { - "Package": "lambda.r", - "Version": "1.2.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "formatR" - ], - "Hash": "b1e925c4b9ffeb901bacf812cbe9a6ad" - }, - "later": { - "Package": "later", - "Version": "1.3.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Rcpp", - "rlang" - ], - "Hash": "40401c9cf2bc2259dfe83311c9384710" - }, - "lattice": { - "Package": "lattice", - "Version": "0.22-5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "grid", - "stats", - "utils" - ], - "Hash": "7c5e89f04e72d6611c77451f6331a091" - }, - "lazyeval": { - "Package": "lazyeval", - "Version": "0.2.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "d908914ae53b04d4c0c0fd72ecc35370" - }, - "lifecycle": { - "Package": "lifecycle", - "Version": "1.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "rlang" - ], - "Hash": "001cecbeac1cff9301bdc3775ee46a86" - }, - "limma": { - "Package": "limma", - "Version": "3.56.2", - "Source": "Bioconductor", - "Requirements": [ - "R", - "grDevices", - "graphics", - "methods", - "stats", - "utils" - ], - "Hash": "15b74284b9eb4641fa99a01e445a8256" - }, - "locfit": { - "Package": "locfit", - "Version": "1.5-9.8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "lattice" - ], - "Hash": "3434988413fbabfdb0fcd6067d7e1aa4" - }, - "magrittr": { - "Package": "magrittr", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "7ce2733a9826b3aeb1775d56fd305472" - }, - "matrixStats": { - "Package": "matrixStats", - "Version": "1.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "9143629fd64335aac6a6250d1c1ed82a" - }, - "memoise": { - "Package": "memoise", - "Version": "2.0.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cachem", - "rlang" - ], - "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" - }, - "mgcv": { - "Package": "mgcv", - "Version": "1.9-0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "Matrix", - "R", - "graphics", - "methods", - "nlme", - "splines", - "stats", - "utils" - ], - "Hash": "086028ca0460d0c368028d3bda58f31b" - }, - "microbenchmark": { - "Package": "microbenchmark", - "Version": "1.4.10", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "graphics", - "stats" - ], - "Hash": "db81b552e393ed092872cf7023469bc2" - }, - "mime": { - "Package": "mime", - "Version": "0.12", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "tools" - ], - "Hash": "18e9c28c1d3ca1560ce30658b22ce104" - }, - "miniUI": { - "Package": "miniUI", - "Version": "0.1.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "htmltools", - "shiny", - "utils" - ], - "Hash": "fec5f52652d60615fdb3957b3d74324a" - }, - "msigdbr": { - "Package": "msigdbr", - "Version": "7.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "babelgene", - "dplyr", - "magrittr", - "rlang", - "tibble", - "tidyselect" - ], - "Hash": "2def1d52dfe1044f82e75d25fb5dd2e5" - }, - "munsell": { - "Package": "munsell", - "Version": "0.5.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "colorspace", - "methods" - ], - "Hash": "6dfe8bf774944bd5595785e3229d8771" - }, - "mvtnorm": { - "Package": "mvtnorm", - "Version": "1.2-3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats" - ], - "Hash": "463b268710930f7bffef33147400966a" - }, - "nlme": { - "Package": "nlme", - "Version": "3.1-163", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "graphics", - "lattice", - "stats", - "utils" - ], - "Hash": "8d1938040a05566f4f7a14af4feadd6b" - }, - "numDeriv": { - "Package": "numDeriv", - "Version": "2016.8-1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "df58958f293b166e4ab885ebcad90e02" - }, - "openssl": { - "Package": "openssl", - "Version": "2.1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "askpass" - ], - "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5" - }, - "org.Hs.eg.db": { - "Package": "org.Hs.eg.db", - "Version": "3.17.0", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "R", - "methods" - ], - "Hash": "bc5b9e048c58ce45bb646c10d311d1e2" - }, - "org.Mm.eg.db": { - "Package": "org.Mm.eg.db", - "Version": "3.17.0", - "Source": "Bioconductor", - "Requirements": [ - "AnnotationDbi", - "R", - "methods" - ], - "Hash": "a78df53519d3e976b4269414bddc2513" - }, - "patchwork": { - "Package": "patchwork", - "Version": "1.1.3", - "Source": "Repository", - "Repository": "RSPM", - "Requirements": [ - "cli", - "ggplot2", - "grDevices", - "graphics", - "grid", - "gtable", - "rlang", - "stats", - "utils" - ], - "Hash": "c5754106c02e8e019941100c81149431" - }, - "pillar": { - "Package": "pillar", - "Version": "1.9.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cli", - "fansi", - "glue", - "lifecycle", - "rlang", - "utf8", - "utils", - "vctrs" - ], - "Hash": "15da5a8412f317beeee6175fbc76f4bb" - }, - "pkgconfig": { - "Package": "pkgconfig", - "Version": "2.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "01f28d4278f15c76cddbea05899c5d6f" - }, - "plogr": { - "Package": "plogr", - "Version": "0.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "09eb987710984fc2905c7129c7d85e65" - }, - "plyr": { - "Package": "plyr", - "Version": "1.8.9", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp" - ], - "Hash": "6b8177fd19982f0020743fadbfdbd933" - }, - "png": { - "Package": "png", - "Version": "0.1-8", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "bd54ba8a0a5faded999a7aab6e46b374" - }, - "polyclip": { - "Package": "polyclip", - "Version": "1.10-6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "436542aadb70675e361cf359285af7c7" - }, - "preprocessCore": { - "Package": "preprocessCore", - "Version": "1.62.1", - "Source": "Bioconductor", - "Requirements": [ - "stats" - ], - "Hash": "b730f86674105ef376e99152aa5226ae" - }, - "promises": { - "Package": "promises", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "Rcpp", - "fastmap", - "later", - "magrittr", - "rlang", - "stats" - ], - "Hash": "0d8a15c9d000970ada1ab21405387dee" - }, - "purrr": { - "Package": "purrr", - "Version": "1.0.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "lifecycle", - "magrittr", - "rlang", - "vctrs" - ], - "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc" - }, - "qvalue": { - "Package": "qvalue", - "Version": "2.32.0", - "Source": "Bioconductor", - "Requirements": [ - "R", - "ggplot2", - "grid", - "reshape2", - "splines" - ], - "Hash": "d07f7cf42c6415334ebc6867b6eed588" - }, - "rappdirs": { - "Package": "rappdirs", - "Version": "0.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "5e3c5dc0b071b21fa128676560dbe94d" - }, - "renv": { - "Package": "renv", - "Version": "1.0.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "utils" - ], - "Hash": "41b847654f567341725473431dd0d5ab" - }, - "reshape2": { - "Package": "reshape2", - "Version": "1.4.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "plyr", - "stringr" - ], - "Hash": "bb5996d0bd962d214a11140d77589917" - }, - "rintrojs": { - "Package": "rintrojs", - "Version": "0.3.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "jsonlite", - "shiny" - ], - "Hash": "22b1346426a5dbed5725ace115be32ca" - }, - "rjson": { - "Package": "rjson", - "Version": "0.2.21", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "f9da75e6444e95a1baf8ca24909d63b9" - }, - "rlang": { - "Package": "rlang", - "Version": "1.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "50a6dbdc522936ca35afc5e2082ea91b" - }, - "rmarkdown": { - "Package": "rmarkdown", - "Version": "2.25", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "bslib", - "evaluate", - "fontawesome", - "htmltools", - "jquerylib", - "jsonlite", - "knitr", - "methods", - "stringr", - "tinytex", - "tools", - "utils", - "xfun", - "yaml" - ], - "Hash": "d65e35823c817f09f4de424fcdfa812a" - }, - "sass": { - "Package": "sass", - "Version": "0.4.7", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "fs", - "htmltools", - "rappdirs", - "rlang" - ], - "Hash": "6bd4d33b50ff927191ec9acbf52fd056" - }, - "scales": { - "Package": "scales", - "Version": "1.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "RColorBrewer", - "farver", - "labeling", - "lifecycle", - "munsell", - "rlang", - "viridisLite" - ], - "Hash": "906cb23d2f1c5680b8ce439b44c6fa63" - }, - "scatterpie": { - "Package": "scatterpie", - "Version": "0.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "dplyr", - "ggforce", - "ggfun", - "ggplot2", - "rlang", - "stats", - "tidyr", - "utils" - ], - "Hash": "a272b0f2f06b3aa01fa4f5a033f0cf4a" - }, - "shadowtext": { - "Package": "shadowtext", - "Version": "0.1.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", - "grid", - "scales" - ], - "Hash": "e639c0fa75fc71085c37e21e05a06e41" - }, - "shape": { - "Package": "shape", - "Version": "1.4.6", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "stats" - ], - "Hash": "9067f962730f58b14d8ae54ca885509f" - }, - "shiny": { - "Package": "shiny", - "Version": "1.7.5.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "R6", - "bslib", - "cachem", - "commonmark", - "crayon", - "ellipsis", - "fastmap", - "fontawesome", - "glue", - "grDevices", - "htmltools", - "httpuv", - "jsonlite", - "later", - "lifecycle", - "methods", - "mime", - "promises", - "rlang", - "sourcetools", - "tools", - "utils", - "withr", - "xtable" - ], - "Hash": "5ec01cc255f2138fc2f0dc74d2b1a1a1" - }, - "shinyAce": { - "Package": "shinyAce", - "Version": "0.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "jsonlite", - "shiny", - "tools", - "utils" - ], - "Hash": "99b2ee37c4f174539b1b0d920b00d16c" - }, - "shinyWidgets": { - "Package": "shinyWidgets", - "Version": "0.8.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "anytime", - "bslib", - "grDevices", - "htmltools", - "jsonlite", - "rlang", - "sass", - "shiny" - ], - "Hash": "c6acc72327e63668bbc7bd258ee54132" - }, - "shinydashboard": { - "Package": "shinydashboard", - "Version": "0.7.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "htmltools", - "promises", - "shiny", - "utils" - ], - "Hash": "e418b532e9bb4eb22a714b9a9f1acee7" - }, - "shinyjs": { - "Package": "shinyjs", - "Version": "2.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "digest", - "jsonlite", - "shiny" - ], - "Hash": "802e4786b353a4bb27116957558548d5" - }, - "snow": { - "Package": "snow", - "Version": "0.4-4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "utils" - ], - "Hash": "40b74690debd20c57d93d8c246b305d4" - }, - "sourcetools": { - "Package": "sourcetools", - "Version": "0.1.7-1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "5f5a7629f956619d519205ec475fe647" - }, - "stringi": { - "Package": "stringi", - "Version": "1.7.12", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats", - "tools", - "utils" - ], - "Hash": "ca8bd84263c77310739d2cf64d84d7c9" - }, - "stringr": { - "Package": "stringr", - "Version": "1.5.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "magrittr", - "rlang", - "stringi", - "vctrs" - ], - "Hash": "671a4d384ae9d32fc47a14e98bfa3dc8" - }, - "sys": { - "Package": "sys", - "Version": "3.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "3a1be13d68d47a8cd0bfd74739ca1555" - }, - "systemfonts": { - "Package": "systemfonts", - "Version": "1.0.5", - "Source": "Repository", - "Repository": "https://carpentries.r-universe.dev", - "Requirements": [ - "R", - "cpp11" - ], - "Hash": "15b594369e70b975ba9f064295983499" - }, - "tibble": { - "Package": "tibble", - "Version": "3.2.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "fansi", - "lifecycle", - "magrittr", - "methods", - "pillar", - "pkgconfig", - "rlang", - "utils", - "vctrs" - ], - "Hash": "a84e2cc86d07289b3b6f5069df7a004c" - }, - "tidygraph": { - "Package": "tidygraph", - "Version": "1.2.3", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "cli", - "cpp11", - "dplyr", - "igraph", - "magrittr", - "pillar", - "rlang", - "stats", - "tibble", - "tidyr", - "tools", - "utils" - ], - "Hash": "0fc97a52b4b32a0b4a3de4c5241348e2" - }, - "tidyr": { - "Package": "tidyr", - "Version": "1.3.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "cpp11", - "dplyr", - "glue", - "lifecycle", - "magrittr", - "purrr", - "rlang", - "stringr", - "tibble", - "tidyselect", - "utils", - "vctrs" - ], - "Hash": "e47debdc7ce599b070c8e78e8ac0cfcf" - }, - "tidyselect": { - "Package": "tidyselect", - "Version": "1.2.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "rlang", - "vctrs", - "withr" - ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" - }, - "tidytree": { - "Package": "tidytree", - "Version": "0.4.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ape", - "cli", - "dplyr", - "lazyeval", - "magrittr", - "methods", - "pillar", - "rlang", - "tibble", - "tidyr", - "tidyselect", - "yulab.utils" - ], - "Hash": "b6c0b32b3632419e1a91bf4e0c4f7337" - }, - "tinytex": { - "Package": "tinytex", - "Version": "0.48", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "xfun" - ], - "Hash": "8f96d229b7311beb32b94cf413b13f84" - }, - "treeio": { - "Package": "treeio", - "Version": "1.27.0", - "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "GuangchuangYu", - "RemoteRepo": "treeio", - "RemoteRef": "devel", - "RemoteSha": "a8b64d4a3ac47406684f573f6e94080ff1e95b2d", - "Requirements": [ - "R", - "ape", - "dplyr", - "jsonlite", - "magrittr", - "methods", - "rlang", - "stats", - "tibble", - "tidytree", - "utils" - ], - "Hash": "cdce4cde2d2f25f0de840b9b344c2303" - }, - "tweenr": { - "Package": "tweenr", - "Version": "2.0.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11", - "farver", - "magrittr", - "rlang", - "vctrs" - ], - "Hash": "c16efcef4c72d3bff5e65031f3f1f841" - }, - "utf8": { - "Package": "utf8", - "Version": "1.2.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "62b65c52671e6665f803ff02954446e9" - }, - "vctrs": { - "Package": "vctrs", - "Version": "0.6.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "rlang" - ], - "Hash": "266c1ca411266ba8f365fcc726444b87" - }, - "vipor": { - "Package": "vipor", - "Version": "0.4.5", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "graphics", - "stats" - ], - "Hash": "ea85683da7f2bfa63a98dc6416892591" - }, - "viridis": { - "Package": "viridis", - "Version": "0.6.4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "ggplot2", - "gridExtra", - "viridisLite" - ], - "Hash": "80cd127bc8c9d3d9f0904ead9a9102f1" - }, - "viridisLite": { - "Package": "viridisLite", - "Version": "0.4.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" - ], - "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" - }, - "vsn": { - "Package": "vsn", - "Version": "3.68.0", - "Source": "Bioconductor", - "Requirements": [ - "Biobase", - "R", - "affy", - "ggplot2", - "lattice", - "limma", - "methods" - ], - "Hash": "dc93221cb7cf860a86e60c28ef9db2ca" - }, - "withr": { - "Package": "withr", - "Version": "2.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics", - "stats" - ], - "Hash": "4b25e70111b7d644322e9513f403a272" - }, - "xfun": { - "Package": "xfun", - "Version": "0.41", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "stats", - "tools" - ], - "Hash": "460a5e0fe46a80ef87424ad216028014" - }, - "xtable": { - "Package": "xtable", - "Version": "1.8-4", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "stats", - "utils" - ], - "Hash": "b8acdf8af494d9ec19ccb2481a9b11c2" - }, - "yaml": { - "Package": "yaml", - "Version": "2.3.7", - "Source": "Repository", - "Repository": "CRAN", - "Hash": "0d0056cc5383fbc240ccd0cb584bf436" - }, - "yulab.utils": { - "Package": "yulab.utils", - "Version": "0.1.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "cli", - "digest", - "fs", - "memoise", - "rlang", - "stats", - "tools", - "utils" - ], - "Hash": "792b3c5bc98f04a7d49cbd8c55fe0770" - }, - "zlibbioc": { - "Package": "zlibbioc", - "Version": "1.46.0", - "Source": "Bioconductor", - "Hash": "20158ef5adb641f0b4e8d63136f0e870" - } - } -}