{ "_id": "6a38edf33efcd9bda443cd64", "Package": "TcGSA", "Type": "Package", "Title": "Time-Course Gene Set Analysis", "Version": "0.12.13", "Date": "2025-07-22", "Authors@R": "c(person(c(\"Boris\", \"P\"), \"Hejblum\", role = c(\"aut\", \"cre\"),\nemail = \"boris.hejblum@u-bordeaux.fr\"),\nperson(\"Damien\", \"Chimits\", role = c(\"aut\")),\nperson(\"Anthony\", \"Devaux\", role = c(\"aut\"))\n)", "Description": "Implementation of Time-course Gene Set Analysis (TcGSA), a\nmethod for analyzing longitudinal gene-expression data at the\ngene set level. Method is detailed in: Hejblum, Skinner &\nThiebaut (2015) .", "License": "GPL-2 | file LICENSE", "Encoding": "UTF-8", "BugReports": "https://github.com/sistm/TcGSA/issues", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "URL": "http://sistm.github.io/TcGSA/", "Config/pak/sysreqs": "cmake make libicu-dev", "Repository": "https://sistm.r-universe.dev", "Date/Publication": "2025-07-26 23:41:58 UTC", "RemoteUrl": "https://github.com/sistm/tcgsa", "RemoteRef": "HEAD", "RemoteSha": "0c8885d12127c1cd7c05affb43e820287d4dffad", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-22 08:06:26 UTC", "User": "root" }, "Author": "Boris P Hejblum [aut, cre],\nDamien Chimits [aut],\nAnthony Devaux [aut]", "Maintainer": "Boris P Hejblum ", "MD5sum": "ef68dae68695cb1588f59457d837db47", "_user": "sistm", "_type": "src", "_file": "TcGSA_0.12.13.tar.gz", "_fileid": "dd087724203fc0b409c780a3ce3b1e5173991cb4f668de445c0c87e81add0d1a", "_filesize": 1094834, "_sha256": "dd087724203fc0b409c780a3ce3b1e5173991cb4f668de445c0c87e81add0d1a", "_created": "2026-06-22T08:06:26.000Z", "_published": "2026-06-22T08:10:27.096Z", "_distro": "noble", "_jobs": [ { "job": 82665961571, "time": 194, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7786563236" }, { "job": 82665961529, "time": 194, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7786563412" }, { "job": 82665961542, "time": 113, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7786536490" }, { "job": 82665961553, "time": 150, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7786548927" }, { "job": 82664539410, "time": 515, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7786496048" }, { "job": 82665961543, "time": 141, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7786545820" }, { "job": 82665961561, "time": 142, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7786546452" }, { "job": 82665961567, "time": 138, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7786545401" }, { "job": 82665961558, "time": 122, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7786539690" } ], "_buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/sistm/tcgsa", "_commit": { "id": "0c8885d12127c1cd7c05affb43e820287d4dffad", "author": "borishejblum ", "committer": "borishejblum ", "message": "fancier cli in GHA\n", "time": 1753573318 }, "_maintainer": { "name": "Boris P Hejblum", "email": "boris.hejblum@u-bordeaux.fr", "login": "borishejblum", "description": "", "uuid": 5277851 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.2", "role": "Depends" }, { "package": "ggplot2", "version": ">= 2.0.0", "role": "Depends" }, { "package": "lme4", "version": ">= 1.0-4", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "GSA", "role": "Imports" }, { "package": "multtest", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "gtools", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "splines", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "foreach", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "doParallel", "role": "Suggests" }, { "package": "dearseq", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "GEOquery", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "sistm", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-30", "n": 22 } ], "_tags": [], "_stars": 6, "_contributors": [ { "user": "borishejblum", "count": 169, "uuid": 5277851 }, { "user": "damienchimits", "count": 6, "uuid": 7314390 }, { "user": "anthonydevaux", "count": 1, "uuid": 38243147 } ], "_userbio": { "uuid": 38222472, "type": "organization", "name": "SISTM", "followers": 5, "description": "research team from Inserm BPH U1219 & Inria BSO" }, "_downloads": { "count": 372, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/TcGSA" }, "_mentions": 4, "_devurl": "https://github.com/sistm/tcgsa", "_pkgdown": "http://sistm.github.io/TcGSA/", "_searchresults": 0, "_rbuild": "4.6.0", "_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/TcGSA.html", "LICENSE", "manual.pdf" ], "_homeurl": "https://github.com/sistm/tcgsa", "_realowner": "sistm", "_cranurl": true, "_releases": [ { "version": "0.9.8", "date": "2014-04-28" }, { "version": "0.10.1", "date": "2015-12-22" }, { "version": "0.10.5", "date": "2017-05-03" }, { "version": "0.11.1", "date": "2018-06-08" }, { "version": "0.12.2", "date": "2019-01-16" }, { "version": "0.12.4", "date": "2019-04-30" }, { "version": "0.12.7", "date": "2020-01-24" }, { "version": "0.12.10", "date": "2022-02-28" }, { "version": "0.12.13", "date": "2025-07-22" } ], "_exports": [ "clustTrend", "dchisqmix", "multtest.TcGSA", "pchisqmix", "plot1GS", "plotFit.GS", "plotMultipleGS", "plotPat.1GS", "plotPat.TcGSA", "plotSelect.GS", "qchisqmix", "rchisqmix", "signifLRT.TcGSA", "TcGSA.LR", "TcGSA.LR.parallel" ], "_datasets": [ { "name": "design", "title": "Simulated Data for TcGSA", "object": "data_simu_TcGSA", "file": "data_simu_TcGSA.RData", "class": [ "data.frame" ], "fields": [ "Patient_ID", "TimePoint", "Sample_name", "group.var", "Group_ID_paired" ], "rows": 50, "table": true, "tojson": true }, { "name": "expr_1grp", "title": "Simulated Data for TcGSA", "object": "data_simu_TcGSA", "file": "data_simu_TcGSA.RData", "class": [ "data.frame" ], "fields": [ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50" ], "rows": 250, "table": true, "tojson": true }, { "name": "expr_2grp", "title": "Simulated Data for TcGSA", "object": "data_simu_TcGSA", "file": "data_simu_TcGSA.RData", "class": [ "data.frame" ], "fields": [ "1", "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46", "47", "48", "49", "50" ], "rows": 250, "table": true, "tojson": true }, { "name": "gmt_sim", "title": "Simulated Data for TcGSA", "object": "data_simu_TcGSA", "file": "data_simu_TcGSA.RData", "class": [ "GSA.genesets" ], "fields": [], "table": true, "tojson": false } ], "_help": [ { "page": "TcGSA-package", "title": "Time-course Gene Set Analysis", "topics": [ "TcGSA-package", "TcGSA" ] }, { "page": "clustTrend", "title": "Cluster the genes dynamics into different dominant trends.", "topics": [ "ClusteredTrends", "clustTrend", "plot.ClusteredTrends", "print.ClusteredTrends" ] }, { "page": "data_simu_TcGSA", "title": "Simulated Data for TcGSA", "topics": [ "data_simu_TcGSA", "design", "expr_1grp", "expr_2grp", "gmt_sim" ] }, { "page": "multtest.TcGSA", "title": "Computing the P-value of the Likelihood Ratios Applying a Multiple Testing Correction", "topics": [ "multtest.TcGSA" ] }, { "page": "plot.TcGSA", "title": "Plot a Gene Set Trends Heatmap.", "topics": [ "plot.TcGSA" ] }, { "page": "plot1GS", "title": "Plotting a Specific Gene Set", "topics": [ "plot1GS" ] }, { "page": "plotFit.GS", "title": "Plotting function for exploring the fitness of the mixed modeling used in TcGSA", "topics": [ "plotFit.GS" ] }, { "page": "plotMultipleGS", "title": "Plotting Multiple Gene Sets in a single plot", "topics": [ "plotMultipleGS" ] }, { "page": "plotPat.1GS", "title": "Plotting a Specific Gene Set Stratifying on Patients", "topics": [ "plotPat.1GS" ] }, { "page": "plotPat.TcGSA", "title": "Plot a Gene Set Trends Heatmap for each Patient.", "topics": [ "plotPat.TcGSA" ] }, { "page": "plotSelect.GS", "title": "Plotting (several) Selected Gene Set(s) in some Subjects", "topics": [ "plotSelect.GS" ] }, { "page": "chisqmix", "title": "Chi-Squared Mixtures Distribution", "topics": [ "chisqmix", "dchisqmix", "pchisqmix", "qchisqmix", "rchisqmix" ] }, { "page": "signifLRT.TcGSA", "title": "Identifying the Significant Gene Sets", "topics": [ "signifLRT.TcGSA" ] }, { "page": "summary.TcGSA", "title": "Summarizing TcGSA", "topics": [ "print.summary.TcGSA", "summary.TcGSA" ] }, { "page": "TcGSA.LR", "title": "Computing the Likelihood Ratios for the Gene Sets under Scrutiny", "topics": [ "print.TcGSA", "print.TcGSA.LR", "TcGSA.LR" ] }, { "page": "TcGSA.LR.parallel", "title": "Parallel computing the Likelihood Ratios for the Gene Sets under Scrutiny", "topics": [ "TcGSA.LR.parallel" ] } ], "_readme": "https://github.com/sistm/tcgsa/raw/HEAD/README.md", "_rundeps": [ "Biobase", "BiocGenerics", "boot", "cli", "cluster", "cowplot", "cpp11", "farver", "generics", "ggplot2", "glue", "GSA", "gtable", "gtools", "isoband", "labeling", "lattice", "lifecycle", "lme4", "magrittr", "MASS", "Matrix", "minqa", "multtest", "nlme", "nloptr", "plyr", "R6", "rbibutils", "RColorBrewer", "Rcpp", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "survival", "vctrs", "viridisLite", "withr" ], "_vignettes": [ { "source": "TcGSA_userguide.Rmd", "filename": "TcGSA_userguide.html", "title": "User guide to the TcGSA R package", "author": "Anthony Devaux, Boris Hejblum", "engine": "knitr::rmarkdown", "headings": [ "Overview of TcGSA", "Getting started using TcGSA", "Gene set object", "Download gmts from Hejblum et al., 2015", "Self-built gmt", "Gene expression matrix", "Design data matrix", "How to use TcGSA for one treatment group ?", "Data preparation", "Import of data files", "Likelihood ratios test", "Graphical outputs", "How to use TcGSA for several treatment group ?", "Likelihood ratio tests", "Graphical outputs for significant gene sets", "Make clusters from tcgsa object", "Heatmap of significant gene sets", "References", "Appendix", "GEOquery package" ], "created": "2017-07-27 11:08:11", "modified": "2025-07-22 15:58:56", "commits": 21 } ], "_score": 5.380211241711606, "_indexed": true, "_nocasepkg": "tcgsa", "_universes": [ "sistm", "borishejblum" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.12.13", "date": "2026-06-22T08:09:13.000Z", "distro": "noble", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "f6c7d32d4effe165bbd3b194830ec1756c1a6be3ca88b010d8fafd2035c4d617", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" }, { "r": "4.6.0", "os": "linux", "version": "0.12.13", "date": "2026-06-22T08:09:14.000Z", "distro": "noble", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "85a23d640465b7ea903b4cc8e57238ee24df76919882fc68fec20fd4ce8683ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" }, { "r": "4.5.3", "os": "mac", "version": "0.12.13", "date": "2026-06-22T08:08:16.000Z", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "51998792fea5e91dc7c80c56c6339b91bc6da776f2d7d519feb288126bb07bf5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" }, { "r": "4.6.0", "os": "mac", "version": "0.12.13", "date": "2026-06-22T08:08:42.000Z", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "479defc52fb95710f43a8aa6454f2a21c33311d6427644fa8a39c62f82c0e0f7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" }, { "r": "4.6.0", "os": "wasm", "version": "0.12.13", "date": "2026-06-22T08:09:15.000Z", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "d083ff00e7eb0b246bee58e9bb4aa1563d728458d8f54d9c0e0e20ad9a0fdae1", "status": "success", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" }, { "r": "4.7.0", "os": "win", "version": "0.12.13", "date": "2026-06-22T08:08:06.000Z", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "884c98bd5f29ec752a45f9871060c4c3da319d05427ccac725fef43a62475519", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" }, { "r": "4.5.3", "os": "win", "version": "0.12.13", "date": "2026-06-22T08:08:13.000Z", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "bf835ed1c22eb1c6b80c57c9e71c96bd2bcdf6707388a08860edebdd3e94e2d1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" }, { "r": "4.6.0", "os": "win", "version": "0.12.13", "date": "2026-06-22T08:07:55.000Z", "commit": "0c8885d12127c1cd7c05affb43e820287d4dffad", "fileid": "eae1a0c38ac5be0133d0054fdcadf5b38736545f0881c461d2c04cf5a74c18a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/sistm/actions/runs/27938063563" } ] }