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June 14, 2023 14:34
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| library(abind) | |
| library(annotate) | |
| library(AnnotationDbi) | |
| library(AnnotationFilter) | |
| library(askpass) | |
| library(Azimuth) | |
| library(backports) | |
| library(base64enc) | |
| library(beachmat) | |
| library(BH) | |
| library(Biobase) | |
| library(BiocFileCache) | |
| library(BiocGenerics) | |
| library(BiocIO) | |
| library(BiocManager) | |
| library(BiocParallel) | |
| library(biomaRt) | |
| library(Biostrings) | |
| library(bit) | |
| library(bit64) | |
| library(bitops) | |
| library(blob) | |
| library(boot) | |
| library(BPCells) | |
| library(brio) | |
| library(broom) | |
| library(BSgenome) | |
| library(BSgenome.Hsapiens.UCSC.hg38) | |
| library(bslib) | |
| library(cachem) | |
| library(callr) | |
| library(car) | |
| library(carData) | |
| library(caTools) | |
| library(cellranger) | |
| library(class) | |
| library(cli) | |
| library(clipr) | |
| library(cluster) | |
| library(CNEr) | |
| library(codetools) | |
| library(colorspace) | |
| library(commonmark) | |
| library(corrplot) | |
| library(cowplot) | |
| library(cpp11) | |
| library(crayon) | |
| library(credentials) | |
| library(crosstalk) | |
| library(curl) | |
| library(data.table) | |
| library(DBI) | |
| library(dbplyr) | |
| library(DelayedArray) | |
| library(DelayedMatrixStats) | |
| library(deldir) | |
| library(desc) | |
| library(diffobj) | |
| library(digest) | |
| library(DirichletMultinomial) | |
| library(dotCall64) | |
| library(dplyr) | |
| library(dqrng) | |
| library(DT) | |
| library(ellipsis) | |
| library(EnsDb.Hsapiens.v86) | |
| library(ensembldb) | |
| library(evaluate) | |
| library(fansi) | |
| library(farver) | |
| library(fastDummies) | |
| library(fastmap) | |
| library(fastmatch) | |
| library(filelock) | |
| library(fitdistrplus) | |
| library(FNN) | |
| library(fontawesome) | |
| library(foreign) | |
| library(formatR) | |
| library(fs) | |
| library(futile.logger) | |
| library(futile.options) | |
| library(future) | |
| library(future.apply) | |
| library(gargle) | |
| library(generics) | |
| library(GenomeInfoDb) | |
| library(GenomeInfoDbData) | |
| library(GenomicAlignments) | |
| library(GenomicFeatures) | |
| library(GenomicRanges) | |
| library(gert) | |
| library(ggplot2) | |
| library(ggpubr) | |
| library(ggrepel) | |
| library(ggridges) | |
| library(ggsci) | |
| library(ggsignif) | |
| library(gh) | |
| library(gitcreds) | |
| library(glmGamPoi) | |
| library(globals) | |
| library(glue) | |
| library(GO.db) | |
| library(goftest) | |
| library(googledrive) | |
| library(googlesheets4) | |
| library(gplots) | |
| library(gridExtra) | |
| library(gtable) | |
| library(gtools) | |
| library(HDF5Array) | |
| library(hdf5r) | |
| library(here) | |
| library(hexbin) | |
| library(highr) | |
| library(hms) | |
| library(htmltools) | |
| library(htmlwidgets) | |
| library(httpuv) | |
| library(httr) | |
| library(httr2) | |
| library(ica) | |
| library(ids) | |
| library(igraph) | |
| library(ini) | |
| library(IRanges) | |
| library(irlba) | |
| library(isoband) | |
| library(JASPAR2020) | |
| library(jquerylib) | |
| library(jsonlite) | |
| library(KEGGREST) | |
| library(kernlab) | |
| library(KernSmooth) | |
| library(knitr) | |
| library(labeling) | |
| library(lambda.r) | |
| library(later) | |
| library(lattice) | |
| library(lazyeval) | |
| library(leiden) | |
| library(lifecycle) | |
| library(listenv) | |
| library(lme4) | |
| library(lmtest) | |
| library(magrittr) | |
| library(MASS) | |
| library(Matrix) | |
| library(MatrixGenerics) | |
| library(MatrixModels) | |
| library(matrixStats) | |
| library(memoise) | |
| library(mgcv) | |
| library(mime) | |
| library(miniUI) | |
| library(minqa) | |
| library(mixtools) | |
| library(munsell) | |
| library(nlme) | |
| library(nloptr) | |
| library(nnet) | |
| library(numDeriv) | |
| library(openssl) | |
| library(parallelly) | |
| library(patchwork) | |
| library(pbapply) | |
| library(pbkrtest) | |
| library(pheatmap) | |
| library(pillar) | |
| library(pkgconfig) | |
| library(pkgload) | |
| library(plogr) | |
| library(plotly) | |
| library(plyr) | |
| library(png) | |
| library(polyclip) | |
| library(polynom) | |
| library(poweRlaw) | |
| library(pracma) | |
| library(praise) | |
| library(presto) | |
| library(prettyunits) | |
| library(processx) | |
| library(progress) | |
| library(progressr) | |
| library(promises) | |
| library(ProtGenerics) | |
| library(ps) | |
| library(purrr) | |
| library(quantreg) | |
| library(R6) | |
| library(RANN) | |
| library(rappdirs) | |
| library(RColorBrewer) | |
| library(Rcpp) | |
| library(RcppAnnoy) | |
| library(RcppArmadillo) | |
| library(RcppEigen) | |
| library(RcppHNSW) | |
| library(RcppProgress) | |
| library(RcppRoll) | |
| library(RcppTOML) | |
| library(RCurl) | |
| library(readr) | |
| library(rematch) | |
| library(rematch2) | |
| library(remotes) | |
| library(renv) | |
| library(reshape2) | |
| library(restfulr) | |
| library(reticulate) | |
| library(rhdf5) | |
| library(rhdf5filters) | |
| library(Rhdf5lib) | |
| library(Rhtslib) | |
| library(rjson) | |
| library(rlang) | |
| library(rmarkdown) | |
| library(R.methodsS3) | |
| library(ROCR) | |
| library(R.oo) | |
| library(rootSolve) | |
| library(rpart) | |
| library(rprojroot) | |
| library(Rsamtools) | |
| library(RSpectra) | |
| library(RSQLite) | |
| library(rstatix) | |
| library(rstudioapi) | |
| library(rsvd) | |
| library(rtracklayer) | |
| library(Rtsne) | |
| library(R.utils) | |
| library(S4Arrays) | |
| library(S4Vectors) | |
| library(sass) | |
| library(scales) | |
| library(scattermore) | |
| library(sctransform) | |
| library(segmented) | |
| library(seqLogo) | |
| library(Seurat) | |
| library(SeuratData) | |
| library(SeuratDisk) | |
| library(SeuratObject) | |
| library(SeuratWrappers) | |
| library(shiny) | |
| library(shinyBS) | |
| library(shinydashboard) | |
| library(shinyjs) | |
| library(Signac) | |
| library(SingleCellExperiment) | |
| library(sitmo) | |
| library(snow) | |
| library(SoupX) | |
| library(sourcetools) | |
| library(sp) | |
| library(spam) | |
| library(SparseM) | |
| library(sparseMatrixStats) | |
| library(spatial) | |
| library(spatstat.data) | |
| library(spatstat.explore) | |
| library(spatstat.geom) | |
| library(spatstat.random) | |
| library(spatstat.sparse) | |
| library(spatstat.utils) | |
| library(stringi) | |
| library(stringr) | |
| library(SummarizedExperiment) | |
| library(survival) | |
| library(sys) | |
| library(tensor) | |
| library(testthat) | |
| library(TFBSTools) | |
| library(TFMPvalue) | |
| library(tibble) | |
| library(tidyr) | |
| library(tidyselect) | |
| library(tinytex) | |
| library(tzdb) | |
| library(utf8) | |
| library(uuid) | |
| library(uwot) | |
| library(vctrs) | |
| library(viridisLite) | |
| library(vroom) | |
| library(waldo) | |
| library(wesanderson) | |
| library(whisker) | |
| library(withr) | |
| library(xfun) | |
| library(XML) | |
| library(xml2) | |
| library(xtable) | |
| library(XVector) | |
| library(yaml) | |
| library(zip) | |
| library(zlibbioc) | |
| library(zoo) |
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| { | |
| "R": { | |
| "Version": "4.3.0", | |
| "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": "CRAN", | |
| "URL": "https://cloud.r-project.org" | |
| } | |
| ] | |
| }, | |
| "Bioconductor": { | |
| "Version": "3.17" | |
| }, | |
| "Packages": { | |
| "AnnotationDbi": { | |
| "Package": "AnnotationDbi", | |
| "Version": "1.62.1", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/AnnotationDbi", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "21f8479", | |
| "git_last_commit_date": "2023-05-01", | |
| "Requirements": [ | |
| "Biobase", | |
| "BiocGenerics", | |
| "DBI", | |
| "IRanges", | |
| "KEGGREST", | |
| "R", | |
| "RSQLite", | |
| "S4Vectors", | |
| "methods", | |
| "stats", | |
| "stats4" | |
| ], | |
| "Hash": "23a8bf8b555ec9e4d20c8a0bec495786" | |
| }, | |
| "AnnotationFilter": { | |
| "Package": "AnnotationFilter", | |
| "Version": "1.24.0", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/AnnotationFilter", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "172d9c1", | |
| "git_last_commit_date": "2023-04-25", | |
| "Requirements": [ | |
| "GenomicRanges", | |
| "R", | |
| "lazyeval", | |
| "methods", | |
| "utils" | |
| ], | |
| "Hash": "5ee6a8b3d2ebe0eff2149c526dda4b64" | |
| }, | |
| "Azimuth": { | |
| "Package": "Azimuth", | |
| "Version": "0.4.6.9004", | |
| "Source": "GitHub", | |
| "Remotes": "immunogenomics/presto, satijalab/seurat-data@seurat5, mojaveazure/seurat-object@seurat5, stuart-lab/signac@seurat5", | |
| "RemoteType": "github", | |
| "RemoteHost": "api.github.com", | |
| "RemoteRepo": "azimuth", | |
| "RemoteUsername": "satijalab", | |
| "RemoteRef": "seurat5", | |
| "RemoteSha": "f50f441fef7ec5d69363dd08055f0f8a6e4f8808", | |
| "Requirements": [ | |
| "BSgenome.Hsapiens.UCSC.hg38", | |
| "DT", | |
| "EnsDb.Hsapiens.v86", | |
| "JASPAR2020", | |
| "Matrix", | |
| "R", | |
| "Rcpp", | |
| "Seurat", | |
| "SeuratData", | |
| "SeuratDisk", | |
| "SeuratObject", | |
| "TFBSTools", | |
| "future", | |
| "ggplot2", | |
| "glmGamPoi", | |
| "googlesheets4", | |
| "hdf5r", | |
| "htmltools", | |
| "httr", | |
| "jsonlite", | |
| "methods", | |
| "patchwork", | |
| "plotly", | |
| "presto", | |
| "rlang", | |
| "scales", | |
| "shiny", | |
| "shinyBS", | |
| "shinydashboard", | |
| "shinyjs", | |
| "stats", | |
| "stringr", | |
| "tools", | |
| "utils", | |
| "withr" | |
| ], | |
| "Hash": "e8e8f6598dad975cc9c15252e47be76c" | |
| }, | |
| "BH": { | |
| "Package": "BH", | |
| "Version": "1.81.0-1", | |
| "Source": "Repository", | |
| "Repository": "CRAN", | |
| "Hash": "68122010f01c4dcfbe58ce7112f2433d" | |
| }, | |
| "BPCells": { | |
| "Package": "BPCells", | |
| "Version": "0.1.0", | |
| "Source": "GitHub", | |
| "RemoteType": "github", | |
| "RemoteHost": "api.github.com", | |
| "RemoteRepo": "BPCells", | |
| "RemoteUsername": "bnprks", | |
| "RemoteRef": "HEAD", | |
| "RemoteSha": "9d1a4ca6f3ac4fc39872cc44a21333aff578937f", | |
| "Requirements": [ | |
| "Matrix", | |
| "R", | |
| "RColorBrewer", | |
| "Rcpp", | |
| "RcppEigen", | |
| "dplyr", | |
| "ggplot2", | |
| "ggrepel", | |
| "grDevices", | |
| "hexbin", | |
| "magrittr", | |
| "methods", | |
| "patchwork", | |
| "rlang", | |
| "scales", | |
| "scattermore", | |
| "stringr", | |
| "tibble", | |
| "tidyr", | |
| "vctrs" | |
| ], | |
| "Hash": "708b112f78f05dc98ace4a0259e5d5d3" | |
| }, | |
| "BSgenome": { | |
| "Package": "BSgenome", | |
| "Version": "1.68.0", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/BSgenome", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "c546020", | |
| "git_last_commit_date": "2023-04-25", | |
| "Requirements": [ | |
| "BiocGenerics", | |
| "Biostrings", | |
| "GenomeInfoDb", | |
| "GenomicRanges", | |
| "IRanges", | |
| "R", | |
| "Rsamtools", | |
| "S4Vectors", | |
| "XVector", | |
| "matrixStats", | |
| "methods", | |
| "rtracklayer", | |
| "stats", | |
| "utils" | |
| ], | |
| "Hash": "9d7c3c9b904c28bc971ed29d3f3b445e" | |
| }, | |
| "BSgenome.Hsapiens.UCSC.hg38": { | |
| "Package": "BSgenome.Hsapiens.UCSC.hg38", | |
| "Version": "1.4.5", | |
| "Source": "Bioconductor", | |
| "Requirements": [ | |
| "BSgenome", | |
| "GenomeInfoDb", | |
| "R" | |
| ], | |
| "Hash": "0ba28cc20a4f8629fbb30d0bf1a133ac" | |
| }, | |
| "Biobase": { | |
| "Package": "Biobase", | |
| "Version": "2.60.0", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/Biobase", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "8dc10d2", | |
| "git_last_commit_date": "2023-04-25", | |
| "Requirements": [ | |
| "BiocGenerics", | |
| "R", | |
| "methods", | |
| "utils" | |
| ], | |
| "Hash": "ed269b250f5844d54dfdc7e749f901aa" | |
| }, | |
| "BiocFileCache": { | |
| "Package": "BiocFileCache", | |
| "Version": "2.8.0", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/BiocFileCache", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "d088b32", | |
| "git_last_commit_date": "2023-04-25", | |
| "Requirements": [ | |
| "DBI", | |
| "R", | |
| "RSQLite", | |
| "curl", | |
| "dbplyr", | |
| "dplyr", | |
| "filelock", | |
| "httr", | |
| "methods", | |
| "stats", | |
| "utils" | |
| ], | |
| "Hash": "4fcebdf379954d5d1a3291006a93499b" | |
| }, | |
| "BiocGenerics": { | |
| "Package": "BiocGenerics", | |
| "Version": "0.46.0", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/BiocGenerics", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "a90f0c5", | |
| "git_last_commit_date": "2023-04-25", | |
| "Requirements": [ | |
| "R", | |
| "graphics", | |
| "methods", | |
| "stats", | |
| "utils" | |
| ], | |
| "Hash": "c179ae59955c36f5d0068ed29ce832f7" | |
| }, | |
| "BiocIO": { | |
| "Package": "BiocIO", | |
| "Version": "1.10.0", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/BiocIO", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "1368ff1", | |
| "git_last_commit_date": "2023-04-25", | |
| "Requirements": [ | |
| "BiocGenerics", | |
| "R", | |
| "S4Vectors", | |
| "methods", | |
| "tools" | |
| ], | |
| "Hash": "a236af72143f9023b2f9f5f8baa81712" | |
| }, | |
| "BiocManager": { | |
| "Package": "BiocManager", | |
| "Version": "1.30.21", | |
| "Source": "Repository", | |
| "Repository": "CRAN", | |
| "Requirements": [ | |
| "utils" | |
| ], | |
| "Hash": "be203e7eea75514bc1a41c1de39a9bb9" | |
| }, | |
| "BiocParallel": { | |
| "Package": "BiocParallel", | |
| "Version": "1.34.2", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/BiocParallel", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "77491b2", | |
| "git_last_commit_date": "2023-05-22", | |
| "Requirements": [ | |
| "BH", | |
| "R", | |
| "codetools", | |
| "cpp11", | |
| "futile.logger", | |
| "methods", | |
| "parallel", | |
| "snow", | |
| "stats", | |
| "utils" | |
| ], | |
| "Hash": "84347b6a8118ba2182b148298b118f0e" | |
| }, | |
| "Biostrings": { | |
| "Package": "Biostrings", | |
| "Version": "2.68.1", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/Biostrings", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "cfbb402", | |
| "git_last_commit_date": "2023-05-16", | |
| "Requirements": [ | |
| "BiocGenerics", | |
| "GenomeInfoDb", | |
| "IRanges", | |
| "R", | |
| "S4Vectors", | |
| "XVector", | |
| "crayon", | |
| "grDevices", | |
| "graphics", | |
| "methods", | |
| "stats", | |
| "utils" | |
| ], | |
| "Hash": "838eef43ab267a7409d68ba0fa8da5fa" | |
| }, | |
| "CNEr": { | |
| "Package": "CNEr", | |
| "Version": "1.36.0", | |
| "Source": "Bioconductor", | |
| "git_url": "https://git.bioconductor.org/packages/CNEr", | |
| "git_branch": "RELEASE_3_17", | |
| "git_last_commit": "4f2feeb", | |
| "git_last_commit_date": "2023-04-25", | |
| "Requirements": [ | |
| "BiocGenerics", | |
| "Biostrings", | |
| "DBI", | |
| "GO.db", | |
| "GenomeInfoDb", | |
| "GenomicAlignments", | |
| "GenomicRanges", | |
| "IRanges", | |
| "KEGGREST", | |
| "R", | |
| "R.utils", | |
| "RSQLite", | |
| "S4Vectors", | |
| "XVector", | |
| "annotate", | |
| "ggplot2", | |
| "methods", | |
| "parallel", | |
| "poweRlaw", | |
| "readr", | |
| "reshape2", | |
| "rtracklayer", | |
| "tools" | |
| ], | |
| "Hash": "1e766280ab3ab287fc581c1db8ab96bf" | |
| }, | |
| "DBI": { | |
| "Package": "DBI", | |
| "Version": "1.1.3", | |
| "Source": "Repository", | |
| "Repository": "CRAN", | |
| "Requirements": [ | |
| "R", | |
| "methods" | |
| ], | |
| "Hash": "b2866e62bab9378c3cc9476a1954226b" | |
| }, | |
| "DT": { | |
| "Package": "DT", | |
| "Version": "0.28", | |
| "Source": "Repository", | |
| "Repository": "CRAN", | |
| "Requirements": [ | |
| "crosstalk", | |
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