{ "_id": "6a49414b18cdde069385df8c", "Package": "TMSig", "Type": "Package", "Title": "Tools for Molecular Signatures", "Version": "1.7.0", "Date": "2024-10-17", "Authors@R": "c(\nperson(given = \"Tyler\", family = \"Sagendorf\",\nemail = \"tyler.sagendorf@pnnl.gov\",\ncomment = c(ORCID = \"0000-0003-1552-4870\"),\nrole = c(\"aut\", \"cre\")),\nperson(given = \"Di\", family = \"Wu\", role = \"ctb\"),\nperson(given = \"Gordon\", family = \"Smyth\", role = \"ctb\")\n)", "Description": "The TMSig package contains tools to prepare, analyze, and\nvisualize named lists of sets, with an emphasis on molecular\nsignatures (such as gene or kinase sets). It includes fast,\nmemory efficient functions to construct sparse incidence and\nsimilarity matrices and filter, cluster, invert, and decompose\nsets. Additionally, bubble heatmaps can be created to visualize\nthe results of any differential or molecular signatures\nanalysis.", "License": "GPL (>= 3)", "URL": "https://github.com/EMSL-Computing/TMSig", "BugReports": "https://github.com/EMSL-Computing/TMSig/issues", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "Roxygen": "list(markdown = TRUE)", "VignetteBuilder": "knitr", "biocViews": "Clustering, GeneSetEnrichment, GraphAndNetwork, Pathways,\nVisualization", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev perl zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 13:04:00 UTC", "RemoteUrl": "https://github.com/bioc/TMSig", "RemoteRef": "HEAD", "RemoteSha": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-04 07:53:14 UTC", "User": "root" }, "Author": "Tyler Sagendorf [aut, cre] (ORCID:\n),\nDi Wu [ctb],\nGordon Smyth [ctb]", "Maintainer": "Tyler Sagendorf ", "_user": "bioc", "_type": "src", "_file": "TMSig_1.7.0.tar.gz", "_fileid": "https://r2.ropensci.org/cddef8c033db02044de51c469447f51330536322eb1d98afd910eee2d69a480f", "_filesize": 3904753, "_sha256": "cddef8c033db02044de51c469447f51330536322eb1d98afd910eee2d69a480f", "_expires": "2026-10-12T17:22:17.000Z", "_created": "2026-07-04T07:53:14.000Z", "_published": "2026-07-04T17:22:19.299Z", "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038", "_status": "success", "_upstream": "https://github.com/bioc/TMSig", "_commit": { "id": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381440 }, "_maintainer": { "name": "Tyler Sagendorf", "email": "tyler.sagendorf@pnnl.gov", "orcid": "0000-0003-1552-4870" }, "_distro": "resolute", "_jobs": [ { "job": 85151810105, "time": 180, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "8079810432" }, { "job": 85151810160, "time": 278, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "8079821617" }, { "job": 85151809999, "time": 296, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "8079823720" }, { "job": 85151810108, "time": 170, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "8080149867" }, { "job": 85151810205, "time": 135, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "8080147239" }, { "job": 85151809929, "time": 281, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8079790919" }, { "job": 85151810115, "time": 133, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8079805038" }, { "job": 85151810113, "time": 177, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "8079809996" }, { "job": 85151810161, "time": 178, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "8079810094" }, { "job": 85151810154, "time": 183, "config": "windows-release", "r": "4.6.1", "check": "OK", "artifact": "8079810693" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4.0", "role": "Depends" }, { "package": "limma", "role": "Depends" }, { "package": "circlize", "role": "Imports" }, { "package": "ComplexHeatmap", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "GSEABase", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.7.0", "bioc": "3.24" }, { "branch": "release", "version": "1.6.0", "bioc": "3.23" } ], "_topics": [ "clustering", "genesetenrichment", "graphandnetwork", "pathways", "visualization", "gene-sets", "molecular-signatures" ], "_stars": 5, "_contributors": [ { "user": "tylersagendorf", "count": 111, "uuid": 57922480 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_devurl": "https://github.com/emsl-computing/tmsig", "_searchresults": 49, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/TMSig.html", "manual.pdf" ], "_homeurl": "https://github.com/pnnl/tmsig", "_realowner": "bioc", "_cranurl": false, "_exports": [ "cameraColorFun", "cameraPR.matrix", "clusterSets", "decomposeSets", "enrichmap", "extendRangeNum", "filterSets", "gseaColorFun", "incidenceToList", "invertSets", "readGMT", "similarity", "sparseIncidence" ], "_help": [ { "page": "cameraPR.matrix", "title": "Competitive Gene Set Test Accounting for Inter-gene Correlation", "topics": [ "cameraPR.matrix" ] }, { "page": "clusterSets", "title": "Similarity-Based Clustering of Sets", "topics": [ "clusterSets" ] }, { "page": "decomposeSets", "title": "Decompose Pairs of Overlapping Sets Into 3 Disjoint Parts", "topics": [ "decomposeSets" ] }, { "page": "enrichmap", "title": "Set Enrichment Bubble Heatmap", "topics": [ "enrichmap" ] }, { "page": "enrichmapColorFunctions", "title": "Color Functions for enrichmap", "topics": [ "cameraColorFun", "enrichmapColorFunctions", "gseaColorFun" ] }, { "page": "extendRangeNum", "title": "Extend the Range of Values Out to the Nearest Digit", "topics": [ "extendRangeNum" ] }, { "page": "filterSets", "title": "Filter a Named List of Sets by Size", "topics": [ "filterSets", "filterSets,GeneSet,character,numeric,numeric-method", "filterSets,GeneSetCollection,character,numeric,numeric-method" ] }, { "page": "incidenceToList", "title": "Convert Incidence Matrix to a Named List of Sets", "topics": [ "incidenceToList" ] }, { "page": "invertSets", "title": "Invert a List of Sets, Transposing Sets and Elements", "topics": [ "invertSets", "invertSets,GeneSet-method", "invertSets,GeneSetCollection-method" ] }, { "page": "readGMT", "title": "Read GMT File to a Named List of Sets", "topics": [ "readGMT" ] }, { "page": "similarity", "title": "Construct a Matrix of Pairwise Set Similarity Coefficients", "topics": [ "similarity" ] }, { "page": "sparseIncidence", "title": "Construct a Sparse Incidence Matrix", "topics": [ "sparseIncidence", "sparseIncidence,GeneSet-method", "sparseIncidence,GeneSetCollection-method" ] } ], "_readme": "https://github.com/bioc/TMSig/raw/HEAD/README.md", "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "Biobase", "BiocGenerics", "Biostrings", "bit", "bit64", "blob", "cachem", "circlize", "cli", "clue", "cluster", "codetools", "colorspace", "ComplexHeatmap", "cpp11", "crayon", "curl", "data.table", "DBI", "digest", "doParallel", "fastmap", "foreach", "generics", "GetoptLong", "GlobalOptions", "glue", "graph", "GSEABase", "httr", "IRanges", "iterators", "jsonlite", "KEGGREST", "lattice", "lifecycle", "limma", "Matrix", "matrixStats", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "RColorBrewer", "rjson", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "shape", "statmod", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "TMSig.Rmd", "filename": "TMSig.html", "title": "An Introduction to TMSig", "author": "Tyler J. Sagendorf", "engine": "knitr::rmarkdown", "headings": [ "Read GMT Files", "Filter Sets", "Incidence Matrix", "Set Similarity", "Jaccard", "Overlap/Simpson", "Ōtsuka", "Cluster Similar Sets", "Decompose Sets", "Invert Sets", "Enrichment Analysis", "Simulate Gene Expression Data", "Differential Gene Expression Analysis", "CAMERA-PR", "Bubble Heatmaps", "Session Information", "References" ], "created": "2024-08-12 01:46:54", "modified": "2024-10-17 16:41:11", "commits": 7 } ], "_score": 5.389166084364533, "_indexed": true, "_nocasepkg": "tmsig", "_universes": [ "bioc", "emsl-computing" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.0", "date": "2026-07-04T07:56:34.000Z", "distro": "resolute", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/f0436d6a9756e6a9227644aee0595701e038aa38bd7a7951f3e035c560c98987", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" }, { "r": "4.6.1", "os": "linux", "version": "1.7.0", "date": "2026-07-04T07:56:58.000Z", "distro": "resolute", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/ec1937c7920c194aa09a059406de454bf2460e672dae78b9d04ee034a8343956", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" }, { "r": "4.5.3", "os": "mac", "version": "1.7.0", "date": "2026-07-04T08:43:47.000Z", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/fe7105107315b83afda0ecb76811a62634d49918d1ab80f723f1150de6c8f3bc", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" }, { "r": "4.6.1", "os": "mac", "version": "1.7.0", "date": "2026-07-04T08:43:32.000Z", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/c7db23859d582882ab7b3f4701b6c1c4813d6fa15b33ed1b84bfef8c8162637d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.0", "date": "2026-07-04T07:56:00.000Z", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/1072d60d18b1d53045f33af592cce72e371e4e751bb0a3ad888ee3f35ecd2210", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" }, { "r": "4.7.0", "os": "win", "version": "1.7.0", "date": "2026-07-04T07:54:56.000Z", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/c7e44aea7e343217e6e9b4ff4048ff7dadb363b734122a53fd851a7120598bc0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" }, { "r": "4.5.3", "os": "win", "version": "1.7.0", "date": "2026-07-04T07:54:55.000Z", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/5b023bb512568e263c3199c3dcc26477f387c0fb3180805d57336d2074b86a0c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" }, { "r": "4.6.1", "os": "win", "version": "1.7.0", "date": "2026-07-04T07:54:50.000Z", "commit": "bb2a1ff6f28688dd43e4c1101ae4061e414a3d3b", "fileid": "https://r2.ropensci.org/4deb063f21c1d32134ce47e8770837610d374bd7f390439e630a9a16560999ed", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28699611038" } ] }