{ "_id": "6a5b0a769baadeef8ab4a83e", "Package": "TTMap", "Type": "Package", "Title": "Two-Tier Mapper: a clustering tool based on topological data\nanalysis", "Version": "1.35.0", "Date": "2017-07-12", "Author": "Rachel Jeitziner", "Maintainer": "Rachel Jeitziner ", "Description": "TTMap is a clustering method that groups together samples\nwith the same deviation in comparison to a control group. It is\nspecially useful when the data is small. It is parameter free.", "License": "GPL-2", "biocViews": "Software, Microarray, DifferentialExpression,\nMultipleComparison, Clustering, Classification", "Config/pak/sysreqs": "cmake libfreetype6-dev libglu1-mesa-dev make\ntexlive libpng-dev libuv1-dev libgl1-mesa-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:47:15 UTC", "RemoteUrl": "https://github.com/bioc/TTMap", "RemoteRef": "HEAD", "RemoteSha": "d2b271c7bb6ee4be238a546786fca91b25932660", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-18 05:01:42 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "TTMap_1.35.0.tar.gz", "_fileid": "https://r2.ropensci.org/bba38b081ba95de4465202047189d9c2fe4065c80a6902063d0d986a06556b6b", "_filesize": 1818029, "_sha256": "bba38b081ba95de4465202047189d9c2fe4065c80a6902063d0d986a06556b6b", "_expires": "2026-10-26T05:09:08.000Z", "_created": "2026-07-18T05:01:42.000Z", "_published": "2026-07-18T05:09:10.236Z", "_bioccheck": { "error": 1, "warning": 3, "note": 6 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018", "_status": "success", "_upstream": "https://github.com/bioc/TTMap", "_commit": { "id": "d2b271c7bb6ee4be238a546786fca91b25932660", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380435 }, "_maintainer": { "name": "Rachel Jeitziner", "email": "rachel.jeitziner@epfl.ch" }, "_distro": "resolute", "_jobs": [ { "job": 88046059536, "time": 230, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8425674469" }, { "job": 88046059554, "time": 395, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8425703337" }, { "job": 88046059557, "time": 378, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8425700408" }, { "job": 88046059555, "time": 165, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8425663236" }, { "job": 88046059551, "time": 176, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8425664902" }, { "job": 88045616608, "time": 290, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8425633196" }, { "job": 88046059561, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8425662554" }, { "job": 88046059587, "time": 216, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8425672427" }, { "job": 88046059570, "time": 230, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8425674454" }, { "job": 88046059565, "time": 231, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8425675046" } ], "_registered": true, "_dependencies": [ { "package": "rgl", "role": "Depends" }, { "package": "colorRamps", "role": "Depends" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "Biobase", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "airway", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.35.0", "bioc": "3.24" }, { "branch": "release", "version": "1.34.0", "bioc": "3.23" } ], "_topics": [ "software", "microarray", "differentialexpression", "multiplecomparison", "clustering", "classification" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 447, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 412, "source": "https://www.bioconductor.org/packages/stats/bioc/TTMap" }, "_mentions": 1, "_searchresults": 5, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/TTMap.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "calcul_e", "calcul_e_single", "control_adjustment", "generate_correlation", "generate_euclidean", "generate_mismatch_distance", "generate_p_val_correlation", "generate_single_cell_complete_mismatch", "generate_single_cell_mismatch_with_parameter", "hyperrectangle_deviation_assessment", "make_matrices", "read_pcl", "ttmap", "ttmap_sgn_genes", "write_pcl" ], "_help": [ { "page": "TTMap-package", "title": "Two-Tier Mapper: a clustering tool based on topological data analysis", "topics": [ "TTMap-package", "TTMap" ] }, { "page": "calcul_e", "title": "Calculation of the value of epsilon", "topics": [ "calcul_e", "calcul_e_single" ] }, { "page": "control_adjustment", "title": "Calculates a corrected control group, discovers outliers in it.", "topics": [ "control_adjustment" ] }, { "page": "generate_correlation", "title": "Generates different distance matrices", "topics": [ "generate_correlation", "generate_euclidean", "generate_mismatch_distance", "generate_p_val_correlation", "generate_single_cell_complete_mismatch", "generate_single_cell_mismatch_with_parameter" ] }, { "page": "hyperrectangle_deviation_assessment", "title": "Calculation of deviation components", "topics": [ "hyperrectangle_deviation_assessment" ] }, { "page": "make_matrices", "title": "Prepares the matrices for 'control_adjustment'", "topics": [ "make_matrices" ] }, { "page": "make_matrices-methods", "title": "Prepares the matrices for 'control_adjustment'", "topics": [ "make_matrices,data.frame-method", "make_matrices,ExpressionSet-method", "make_matrices,matrix-method", "make_matrices,RangedSummarizedExperiment-method", "make_matrices,SummarizedExperiment-method", "make_matrices-methods" ] }, { "page": "ttmap", "title": "Visualisation of the clustering", "topics": [ "ttmap" ] }, { "page": "ttmap_sgn_genes", "title": "Gives a list of associated genes per cluster", "topics": [ "ttmap_sgn_genes", "ttmap_sgn_genes_inter", "ttmap_sgn_genes_inter2" ] }, { "page": "write_pcl", "title": "Reading, writing and annotation files", "topics": [ "mat2pcl", "read_pcl", "write_pcl" ] } ], "_readme": "https://github.com/bioc/TTMap/raw/HEAD/README.md", "_rundeps": [ "abind", "base64enc", "Biobase", "BiocGenerics", "bslib", "cachem", "cli", "colorRamps", "DelayedArray", "digest", "evaluate", "fastmap", "fontawesome", "fs", "generics", "GenomicRanges", "highr", "htmltools", "htmlwidgets", "IRanges", "jquerylib", "jsonlite", "knitr", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "R6", "rappdirs", "rgl", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "sass", "Seqinfo", "SparseArray", "SummarizedExperiment", "tinytex", "xfun", "XVector", "yaml" ], "_vignettes": [ { "source": "TTMap.Rnw", "filename": "TTMap.pdf", "title": "Manual for the TTMap library", "engine": "utils::Sweave", "headings": [ "1 Introduction", "2 Prepare the data", "3 TTMap part1: Adjustement of the control group (ctrl_adj)", "4 TTMap part1: Hyperrectangle deviation assessement (hda)", "5 TTMap part2: Global-to-local Mapper (gtlmap)", "6 TTMap: Finding the significant genes (sgn_genes)", "7 Conclusion" ], "created": "2017-11-22 08:28:52", "modified": "2018-02-27 12:35:19", "commits": 21 } ], "_score": 4, "_indexed": true, "_nocasepkg": "ttmap", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-07-18T05:06:08.000Z", "distro": "resolute", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/c17cebf52caf88f7a81ef3aa5d0fc3f04e3a0ed096dd383305c85d5b6e70ae2e", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" }, { "r": "4.6.1", "os": "linux", "version": "1.35.0", "date": "2026-07-18T05:06:08.000Z", "distro": "resolute", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/f8ce2b0da850652c7c89f10583ecbb010930b15cb44519d3a3830c438f422ce3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-07-18T05:03:34.000Z", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/2527d6c64d2feee6dc919b98c95604ec8fb770505e13f456acd5f922656db1c2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" }, { "r": "4.6.1", "os": "mac", "version": "1.35.0", "date": "2026-07-18T05:03:35.000Z", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/06aa9ae136140f6a9c6cf87b49100f81a388b7cb78753190b269b5910fe59a7f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-07-18T05:04:52.000Z", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/4c0399af6c8a456e916e57c281565e7895bf9ca7f6841b95c884df4bfd123e40", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-07-18T05:03:33.000Z", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/1ae9ffd9f86dc932f800f80f09b6fb97d77174924ed3fc7ccbeeedb6a7ff6b3f", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-07-18T05:03:19.000Z", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/e0997c225bfd543c9f71646567aa02b19ab18539122d83066d3957c21a354049", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" }, { "r": "4.6.1", "os": "win", "version": "1.35.0", "date": "2026-07-18T05:03:21.000Z", "commit": "d2b271c7bb6ee4be238a546786fca91b25932660", "fileid": "https://r2.ropensci.org/6f7d2f5942742ef5ed1110d62570f22fa1e743470ea0d6c25a7f1da7684db9ee", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/29631403018" } ] }