{ "_id": "6a1afae21d7bb097a09fc7ef", "Package": "transcriptogramer", "Type": "Package", "Title": "Transcriptional analysis based on transcriptograms", "Version": "1.35.0", "Date": "2019-12-13", "Authors@R": "c(\nperson(\"Diego\", \"Morais\", email = \"vinx@ufrn.edu.br\",\nrole = c(\"aut\", \"cre\")),\nperson(\"Rodrigo\", \"Dalmolin\", email = \"rodrigo.dalmolin@imd.ufrn.br\",\nrole = \"aut\"))", "Description": "R package for transcriptional analysis based on\ntranscriptograms, a method to analyze transcriptomes that\nprojects expression values on a set of ordered proteins,\narranged such that the probability that gene products\nparticipate in the same metabolic pathway exponentially\ndecreases with the increase of the distance between two\nproteins of the ordering. Transcriptograms are, hence, genome\nwide gene expression profiles that provide a global view for\nthe cellular metabolism, while indicating gene sets whose\nexpressions are altered.", "License": "GPL (>= 2)", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "Software, Network, Visualization, SystemsBiology,\nGeneExpression, GeneSetEnrichment, GraphAndNetwork, Clustering,\nDifferentialExpression, Microarray, RNASeq, Transcription,\nImmunoOncology", "RoxygenNote": "6.1.1", "VignetteBuilder": "knitr", "SystemRequirements": "Java Runtime Environment (>= 6)", "URL": "https://github.com/arthurvinx/transcriptogramer", "BugReports": "https://github.com/arthurvinx/transcriptogramer/issues", "Config/pak/sysreqs": "libglpk-dev default-jdk libicu-dev libpng-dev\nlibxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:54 UTC", "RemoteUrl": "https://github.com/bioc/transcriptogramer", "RemoteRef": "HEAD", "RemoteSha": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:50:01 UTC", "User": "root" }, "Author": "Diego Morais [aut, cre],\nRodrigo Dalmolin [aut]", "Maintainer": "Diego Morais ", "MD5sum": "82c54173c9231d4724afa4690bece4e8", "_user": "bioc", "_type": "src", "_file": "transcriptogramer_1.35.0.tar.gz", "_fileid": "d28c18027322c8fb1666f012d3ba6e4bff0b7c34cf06644bbc0942c8f846600b", "_filesize": 3765833, "_sha256": "d28c18027322c8fb1666f012d3ba6e4bff0b7c34cf06644bbc0942c8f846600b", "_created": "2026-05-30T09:50:01.000Z", "_published": "2026-05-30T14:57:38.020Z", "_jobs": [ { "job": 78640783528, "time": 199, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7307541163" }, { "job": 78640783534, "time": 339, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307554603" }, { "job": 78640783566, "time": 342, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307554842" }, { "job": 78640783561, "time": 178, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7309054206" }, { "job": 78640783564, "time": 173, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7309052155" }, { "job": 78639718551, "time": 719, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307309817" }, { "job": 78640783518, "time": 148, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307536156" }, { "job": 78640783585, "time": 563, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307574350" }, { "job": 78640783580, "time": 575, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307575605" }, { "job": 78640783565, "time": 218, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307541337" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/transcriptogramer", "_commit": { "id": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380414 }, "_maintainer": { "name": "Diego Morais", "email": "vinx@ufrn.edu.br", "login": "arthurvinx", "description": "Data Analytics Consultant @ ADP | Ph.D. in Bioinformatics.", "uuid": 21181373 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "biomaRt", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "doSNOW", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "limma", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "progress", "role": "Imports" }, { "package": "RedeR", "role": "Imports" }, { "package": "snow", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "topGO", "role": "Imports" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocGenerics", "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", "network", "visualization", "systemsbiology", "geneexpression", "genesetenrichment", "graphandnetwork", "clustering", "differentialexpression", "microarray", "rnaseq", "transcription", "immunooncology" ], "_stars": 4, "_contributors": [ { "user": "arthurvinx", "count": 146, "uuid": 21181373 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "jwokaty", "count": 2, "uuid": 1744257 }, { "user": "vobencha", "count": 2, "uuid": 2466173 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 427, "source": "https://www.bioconductor.org/packages/stats/bioc/transcriptogramer" }, "_mentions": 2, "_devurl": "https://github.com/arthurvinx/transcriptogramer", "_searchresults": 14, "_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/transcriptogramer.html", "manual.pdf" ], "_homeurl": "https://github.com/arthurvinx/transcriptogramer", "_realowner": "bioc", "_cranurl": false, "_exports": [ "clusterEnrichment", "clusterVisualization", "connectivityProperties", "DE", "differentiallyExpressed", "enrichmentPlot", "orderingProperties", "radius", "radius<-", "Terms", "transcriptogramPreprocess", "transcriptogramStep1", "transcriptogramStep2" ], "_datasets": [ { "name": "association", "title": "Association", "object": "association", "class": [ "data.frame" ], "fields": [ "protein1", "protein2" ], "rows": 648304, "table": true, "tojson": true }, { "name": "DEsymbols", "title": "Dictionary Protein2Symbol", "object": "DEsymbols", "class": [ "data.frame" ], "fields": [ "ensembl_peptide_id", "external_gene_name" ], "rows": 12306, "table": true, "tojson": true }, { "name": "GPL570", "title": "Dictionary Protein2Probe", "object": "GPL570", "class": [ "data.frame" ], "fields": [ "Protein", "Probe" ], "rows": 37020, "table": true, "tojson": true }, { "name": "GSE9988", "title": "Dataset containing expression values", "object": "GSE9988", "class": [ "data.frame" ], "fields": [ "GSM252443.cel.gz", "GSM252444.cel.gz", "GSM252445.cel.gz", "GSM252465.cel.gz", "GSM252466.cel.gz", "GSM252467.cel.gz" ], "rows": 27828, "table": true, "tojson": true }, { "name": "Hs700", "title": "Ordered Homo sapiens proteins of combined score greater than or equal to 700", "object": "Hs700", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Hs800", "title": "Ordered Homo sapiens proteins of combined score greater than or equal to 800", "object": "Hs800", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Hs900", "title": "Ordered Homo sapiens proteins of combined score greater than or equal to 900", "object": "Hs900", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "HsBPTerms", "title": "Dictionary Protein2GO", "object": "HsBPTerms", "class": [ "data.frame" ], "fields": [ "ensembl_peptide_id", "go_id" ], "rows": 125465, "table": true, "tojson": true }, { "name": "Mm700", "title": "Ordered Mus musculus proteins of combined score greater than or equal to 700", "object": "Mm700", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Mm800", "title": "Ordered Mus musculus proteins of combined score greater than or equal to 800", "object": "Mm800", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Mm900", "title": "Ordered Mus musculus proteins of combined score greater than or equal to 900", "object": "Mm900", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Rn700", "title": "Ordered Rattus norvegicus proteins of combined score greater than or equal to 700", "object": "Rn700", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Rn800", "title": "Ordered Rattus norvegicus proteins of combined score greater than or equal to 800", "object": "Rn800", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Rn900", "title": "Ordered Rattus norvegicus proteins of combined score greater than or equal to 900", "object": "Rn900", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Sc700", "title": "Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700", "object": "Sc700", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Sc800", "title": "Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800", "object": "Sc800", "class": [ "character" ], "fields": [], "table": false, "tojson": true }, { "name": "Sc900", "title": "Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900", "object": "Sc900", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "transcriptogramer-package", "title": "Transcriptional analysis based on transcriptograms", "topics": [ "transcriptogramer-package", "transcriptogramer" ] }, { "page": "association", "title": "Association", "topics": [ "association" ] }, { "page": "clusterEnrichment-method", "title": "Term enrichment", "topics": [ "clusterEnrichment", "clusterEnrichment,Transcriptogram-method", "clusterEnrichment-method" ] }, { "page": "clusterVisualization-method", "title": "Displays graphs of the differentially expressed clusters", "topics": [ "clusterVisualization", "clusterVisualization,Transcriptogram-method", "clusterVisualization-method" ] }, { "page": "connectivityProperties-method", "title": "Calculates average graph properties as function of node connectivity", "topics": [ "connectivityProperties", "connectivityProperties,Transcriptogram-method", "connectivityProperties-method" ] }, { "page": "DE-method", "title": "Get DE", "topics": [ "DE", "DE,Transcriptogram-method", "DE-method" ] }, { "page": "DEsymbols", "title": "Dictionary Protein2Symbol", "topics": [ "DEsymbols" ] }, { "page": "differentiallyExpressed-method", "title": "Identify which genes are differentially expressed", "topics": [ "differentiallyExpressed", "differentiallyExpressed,Transcriptogram-method", "differentiallyExpressed-method" ] }, { "page": "enrichmentPlot-method", "title": "Projects Gene Ontology terms on the ordering", "topics": [ "enrichmentPlot", "enrichmentPlot,Transcriptogram-method", "enrichmentPlot-method" ] }, { "page": "GPL570", "title": "Dictionary Protein2Probe", "topics": [ "GPL570" ] }, { "page": "GSE9988", "title": "Dataset containing expression values", "topics": [ "GSE9988" ] }, { "page": "Hs700", "title": "Ordered Homo sapiens proteins of combined score greater than or equal to 700", "topics": [ "Hs700" ] }, { "page": "Hs800", "title": "Ordered Homo sapiens proteins of combined score greater than or equal to 800", "topics": [ "Hs800" ] }, { "page": "Hs900", "title": "Ordered Homo sapiens proteins of combined score greater than or equal to 900", "topics": [ "Hs900" ] }, { "page": "HsBPTerms", "title": "Dictionary Protein2GO", "topics": [ "HsBPTerms" ] }, { "page": "Mm700", "title": "Ordered Mus musculus proteins of combined score greater than or equal to 700", "topics": [ "Mm700" ] }, { "page": "Mm800", "title": "Ordered Mus musculus proteins of combined score greater than or equal to 800", "topics": [ "Mm800" ] }, { "page": "Mm900", "title": "Ordered Mus musculus proteins of combined score greater than or equal to 900", "topics": [ "Mm900" ] }, { "page": "orderingProperties-method", "title": "Calculates graph properties projected on the ordered proteins", "topics": [ "orderingProperties", "orderingProperties,Transcriptogram-method", "orderingProperties-method" ] }, { "page": "radius-method", "title": "Radius", "topics": [ "radius", "radius,Transcriptogram-method", "radius-method", "radius<-", "radius<-,Transcriptogram-method" ] }, { "page": "Rn700", "title": "Ordered Rattus norvegicus proteins of combined score greater than or equal to 700", "topics": [ "Rn700" ] }, { "page": "Rn800", "title": "Ordered Rattus norvegicus proteins of combined score greater than or equal to 800", "topics": [ "Rn800" ] }, { "page": "Rn900", "title": "Ordered Rattus norvegicus proteins of combined score greater than or equal to 900", "topics": [ "Rn900" ] }, { "page": "Sc700", "title": "Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700", "topics": [ "Sc700" ] }, { "page": "Sc800", "title": "Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800", "topics": [ "Sc800" ] }, { "page": "Sc900", "title": "Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900", "topics": [ "Sc900" ] }, { "page": "Terms-method", "title": "Get terms", "topics": [ "Terms", "Terms,Transcriptogram-method", "Terms-method" ] }, { "page": "Transcriptogram-class", "title": "Class Transcriptogram", "topics": [ "Transcriptogram-class" ] }, { "page": "transcriptogramPreprocess", "title": "Creates an object of class Transcriptogram", "topics": [ "transcriptogramPreprocess" ] }, { "page": "transcriptogramStep1-method", "title": "Calculates the average of the expression values related to the same protein", "topics": [ "transcriptogramStep1", "transcriptogramStep1,Transcriptogram-method", "transcriptogramStep1-method" ] }, { "page": "transcriptogramStep2-method", "title": "Calculates the average of the expression values using a sliding window", "topics": [ "transcriptogramStep2", "transcriptogramStep2,Transcriptogram-method", "transcriptogramStep2-method" ] } ], "_rundeps": [ "AnnotationDbi", "askpass", "Biobase", "BiocFileCache", "BiocGenerics", "biomaRt", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "data.table", "DBI", "dbplyr", "doSNOW", "dplyr", "farver", "fastmap", "filelock", "foreach", "generics", "ggplot2", "glue", "GO.db", "graph", "gtable", "hms", "httr", "httr2", "igraph", "IRanges", "isoband", "iterators", "jsonlite", "KEGGREST", "labeling", "lattice", "lifecycle", "limma", "magrittr", "Matrix", "matrixStats", "memoise", "mime", "openssl", "pillar", "pkgconfig", "png", "prettyunits", "progress", "purrr", "R6", "rappdirs", "RColorBrewer", "RedeR", "rlang", "RSQLite", "S4Vectors", "S7", "scales", "Seqinfo", "snow", "SparseM", "statmod", "stringi", "stringr", "sys", "tibble", "tidyr", "tidyselect", "topGO", "utf8", "vctrs", "viridisLite", "withr", "xml2", "XVector" ], "_vignettes": [ { "source": "transcriptogramer.Rmd", "filename": "transcriptogramer.html", "title": "The transcriptogramer user's guide", "author": "Diego Morais, Rodrigo Dalmolin", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Quick start", "Topological analysis", "Transcriptogram", "Gene Ontology enrichment analysis", "Frequently asked questions", "Session info", "References" ], "created": "2017-10-02 22:51:55", "modified": "2020-11-19 19:03:17", "commits": 43 } ], "_score": 4.952308009662126, "_indexed": true, "_nocasepkg": "transcriptogramer", "_universes": [ "bioc", "arthurvinx" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.35.0", "date": "2026-05-30T10:33:26.000Z", "distro": "noble", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "1302c5b4157074d8e71671f978a2d4855d42ef8f3ea363823f17b40222115c50", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" }, { "r": "4.6.0", "os": "linux", "version": "1.35.0", "date": "2026-05-30T10:33:27.000Z", "distro": "noble", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "c3f5c19cef67829acb927b1b724a90176b0b4ef57247e0312f2bb4830184a829", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" }, { "r": "4.5.3", "os": "mac", "version": "1.35.0", "date": "2026-05-30T14:55:47.000Z", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "cfaa349bc7e6de1df77df6d8997653d3a71fe994f379d8cecfd39ad4cab11805", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" }, { "r": "4.6.0", "os": "mac", "version": "1.35.0", "date": "2026-05-30T14:55:30.000Z", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "4c99c3c415ff7d03b158c21d14c06835dbf7f0c0a7e7a28183ef8b4a16b37f25", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" }, { "r": "4.6.0", "os": "wasm", "version": "1.35.0", "date": "2026-05-30T10:32:38.000Z", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "636ce09165baff18e1046bab229ecd414f9190e28e2fbd4d6a012e98c8fdfb24", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" }, { "r": "4.7.0", "os": "win", "version": "1.35.0", "date": "2026-05-30T10:36:47.000Z", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "669d59c8fffbf2817225e40b6efb91e1482bc588fc5e38b80d7f561f87a21bcf", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" }, { "r": "4.5.3", "os": "win", "version": "1.35.0", "date": "2026-05-30T10:36:57.000Z", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "2ef5c99ac71c22c854a6f24900debdfc279b23437c2d2ef1202c33ba0876c06b", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" }, { "r": "4.6.0", "os": "win", "version": "1.35.0", "date": "2026-05-30T10:31:08.000Z", "commit": "d14dd1a87606fe96c6428f8f37b5788fc9b3a6a8", "fileid": "71e9f5a28832ce1e53d1dfc8d9a85310750f386705e6ed9d4352e3bffea072b0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676364506" } ] }