{ "_id": "6a1a74531d7bb097a09d1654", "Package": "BioCor", "Title": "Functional Similarities", "Version": "1.37.0", "Authors@R": "c(\nperson(\"Lluís\", \"Revilla Sancho\", , \"lluis.revilla@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9747-2570\")),\nperson(\"Pau\", \"Sancho-Bru\", role = \"ths\",\ncomment = c(ORCID = \"0000-0001-5569-9259\")),\nperson(\"Juan José Salvatella\", \"Lozano\", role = \"ths\",\ncomment = c(ORCID = \"0000-0001-7613-3908\"))\n)", "Description": "Calculates functional similarities based on the pathways\ndescribed on KEGG and REACTOME or in gene sets. These\nsimilarities can be calculated for pathways or gene sets,\ngenes, or clusters and combined with other similarities. They\ncan be used to improve networks, gene selection, testing\nrelationships...", "License": "MIT + file LICENSE", "URL": "https://bioconductor.org/packages/BioCor, https://biocor.llrs.dev", "BugReports": "https://github.com/llrs/BioCor/issues", "VignetteBuilder": "knitr", "biocViews": "StatisticalMethod, Clustering, GeneExpression, Network,\nPathways, NetworkEnrichment, SystemsBiology", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-US", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libpng-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:45:17 UTC", "RemoteUrl": "https://github.com/bioc/BioCor", "RemoteRef": "HEAD", "RemoteSha": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 06:23:15 UTC", "User": "root" }, "Author": "Lluís Revilla Sancho [aut, cre] (ORCID:\n),\nPau Sancho-Bru [ths] (ORCID: ),\nJuan José Salvatella Lozano [ths] (ORCID:\n)", "Maintainer": "Lluís Revilla Sancho ", "MD5sum": "67b102a19145f036dceeda0fede58ae6", "_user": "bioc", "_type": "src", "_file": "BioCor_1.37.0.tar.gz", "_fileid": "0e8b6b9580afd7235a412db65eda4fc143041c62ad65b135fef87d5556dc061c", "_filesize": 1288712, "_sha256": "0e8b6b9580afd7235a412db65eda4fc143041c62ad65b135fef87d5556dc061c", "_created": "2026-05-29T06:23:15.000Z", "_published": "2026-05-30T05:23:31.865Z", "_jobs": [ { "job": 78626287593, "time": 305, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7284505698" }, { "job": 78626287506, "time": 434, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7284535790" }, { "job": 78626287587, "time": 475, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7284546033" }, { "job": 78626287562, "time": 248, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7284749533" }, { "job": 78626287508, "time": 229, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7284746356" }, { "job": 78626287454, "time": 511, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7284435914" }, { "job": 78626287558, "time": 260, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7284495532" }, { "job": 78626287555, "time": 284, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7284501434" }, { "job": 78626287561, "time": 295, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7284503972" }, { "job": 78626287445, "time": 342, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7305652312" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/BioCor", "_commit": { "id": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380317 }, "_maintainer": { "name": "Lluís Revilla Sancho", "email": "lluis.revilla@gmail.com", "login": "llrs", "mastodon": "@Lluis_Revilla@fosstodon.org", "orcid": "0000-0001-9747-2570", "description": "Bioinformatician, data scientist/engineer making data accessible & useful, be it in pharma, research, open source or government data.", "uuid": 6818218 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.4", "role": "Depends" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "GSEABase", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "airway", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "boot", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "ggplot2", "version": ">= 3.4.1", "role": "Suggests" }, { "package": "GOSemSim", "role": "Suggests" }, { "package": "Hmisc", "role": "Suggests" }, { "package": "knitr", "version": ">= 1.43", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "reactome.db", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.1.5", "role": "Suggests" }, { "package": "WGCNA", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-25", "n": 6 }, { "week": "2025-39", "n": 2 }, { "week": "2025-42", "n": 2 }, { "week": "2025-43", "n": 3 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.37.0", "bioc": "3.24" }, { "branch": "release", "version": "1.36.0", "bioc": "3.23" } ], "_topics": [ "statisticalmethod", "clustering", "geneexpression", "network", "pathways", "networkenrichment", "systemsbiology", "bioconductor-packages", "bioinformatics", "functional-similarity", "gene", "gene-sets", "pathway-analysis", "similarity", "similarity-measurement" ], "_stars": 14, "_contributors": [ { "user": "llrs", "count": 515, "uuid": 6818218 }, { "user": "nturaga", "count": 14, "uuid": 2746443 }, { "user": "jwokaty", "count": 12, "uuid": 1744257 }, { "user": "hpages", "count": 2, "uuid": 8810451 }, { "user": "davidmasp", "count": 2, "uuid": 14033475 }, { "user": "vobencha", "count": 2, "uuid": 2466173 }, { "user": "link-ny", "count": 1, "uuid": 4392950 }, { "user": "lshep", "count": 1, "uuid": 18724380 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 511, "source": "https://www.bioconductor.org/packages/stats/bioc/BioCor" }, "_devurl": "https://github.com/llrs/biocor", "_pkgdown": "https://biocor.llrs.dev", "_searchresults": 5, "_rbuild": "4.6.0", "_assets": [ "extra/BioCor.html", "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", "manual.pdf" ], "_homeurl": "https://github.com/llrs/biocor", "_realowner": "bioc", "_cranurl": false, "_exports": [ "addSimilarities", "AintoB", "clusterGeneSim", "clusterSim", "combinadic", "combineScores", "combineScoresPar", "combineSources", "D2J", "diceSim", "duplicateIndices", "geneSim", "inverseList", "J2D", "mclusterGeneSim", "mclusterSim", "mgeneSim", "mpathSim", "pathSim", "plot_data", "plot_similarity", "removeDup", "seq2mat", "similarities", "weighted.prod", "weighted.sum" ], "_help": [ { "page": "BioCor-package", "title": "BioCor: A package to calculate functional similarities", "topics": [ "BioCor-package", "BioCor" ] }, { "page": "addSimilarities", "title": "Additive integration of similarities", "topics": [ "addSimilarities" ] }, { "page": "AintoB", "title": "Insert a matrix into another", "topics": [ "AintoB" ] }, { "page": "clusterGeneSim", "title": "Similarity score between clusters of genes based on genes similarity", "topics": [ "clusterGeneSim", "clusterGeneSim,character,character,GeneSetCollection-method" ] }, { "page": "clusterSim", "title": "Similarity score between clusters of genes based on pathways similarity", "topics": [ "clusterSim", "clusterSim,character,character,GeneSetCollection-method" ] }, { "page": "combinadic", "title": "i-th combination of n elements taken from r", "topics": [ "combinadic" ] }, { "page": "combineScores", "title": "Combining values", "topics": [ "combineScores", "combineScoresPar" ] }, { "page": "combineSources", "title": "Combine different sources of pathways", "topics": [ "combineSources" ] }, { "page": "conversions", "title": "Convert the similarities formats", "topics": [ "conversions", "D2J", "J2D" ] }, { "page": "diceSim", "title": "Compare pathways", "topics": [ "diceSim" ] }, { "page": "duplicateIndices", "title": "Finds the indices of the duplicated events of a vector", "topics": [ "duplicateIndices" ] }, { "page": "geneSim", "title": "Similarity score genes based on pathways similarity", "topics": [ "geneSim", "geneSim,character,character,GeneSetCollection-method" ] }, { "page": "inverseList", "title": "Invert a list", "topics": [ "inverseList" ] }, { "page": "mclusterGeneSim", "title": "Similarity score between clusters of genes based on genes similarity", "topics": [ "mclusterGeneSim", "mclusterGeneSim,list,GeneSetCollection-method" ] }, { "page": "mclusterSim", "title": "Similarity score between clusters of genes based on pathways similarity", "topics": [ "mclusterSim", "mclusterSim,list,GeneSetCollection-method" ] }, { "page": "mgeneSim", "title": "Similarity score genes based on pathways similarity", "topics": [ "mgeneSim", "mgeneSim,character,GeneSetCollection-method", "mgeneSim,missing,GeneSetCollection-method" ] }, { "page": "mpathSim", "title": "Calculates the Dice similarity between pathways", "topics": [ "mpathSim", "mpathSim,character,GeneSetCollection,ANY-method", "mpathSim,missing,GeneSetCollection,ANY-method", "mpathSim,missing,list,ANY-method", "mpathSim,missing,list,missing-method" ] }, { "page": "pathSim", "title": "Calculates the Dice similarity between pathways", "topics": [ "pathSim", "pathSim,character,character,GeneSetCollection-method" ] }, { "page": "plot_similarity", "title": "The position of the nodes is based on the similarity between them.", "topics": [ "plot_data", "plot_similarity" ] }, { "page": "removeDup", "title": "Remove duplicated rows and columns", "topics": [ "removeDup" ] }, { "page": "seq2mat", "title": "Transforms a vector to a symmetric matrix", "topics": [ "seq2mat" ] }, { "page": "similarities", "title": "Apply a function to a list of similarities", "topics": [ "similarities" ] }, { "page": "weighted", "title": "Weighted operations", "topics": [ "weighted", "weighted.prod", "weighted.sum" ] } ], "_pkglogo": "https://github.com/bioc/BioCor/raw/HEAD/man/figures/logo.svg", "_readme": "https://github.com/bioc/BioCor/raw/HEAD/README.md", "_rundeps": [ "annotate", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocGenerics", "BiocParallel", "Biostrings", "bit", "bit64", "blob", "cachem", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "glue", "graph", "GSEABase", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "Matrix", "memoise", "mime", "openssl", "pkgconfig", "png", "R6", "rlang", "RSQLite", "S4Vectors", "Seqinfo", "snow", "sys", "vctrs", "XML", "xtable", "XVector" ], "_vignettes": [ { "source": "BioCor_1_basics.Rmd", "filename": "BioCor_1_basics.html", "title": "About BioCor", "author": "Lluís Revilla, Juan José Lozano, Pau Sancho-Bru", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Citation", "Installation", "Using BioCor", "Preparation", "Pathway similarities", "Combining values", "Gene similarities", "Gene cluster similarities", "By pathways", "By genes", "Converting similarities", "High volumes of gene similarities", "An example of usage", "Comparing with GOSemSim", "WGCNA and BioCor", "FAQ", "How is defined the pathway similarity?", "Why does BioCor use the dice coefficient and not the Jaccard ?", "How does BioCor combine similarities between several pathways of two genes?", "Why do you recommend using the max method to combine similarities scores for pathways?", "How to detect which functional relationship is more important between two genes?", "How to detect with which genes is my gene of interest related?", "Why isn't available a method for calculating GO similarities?", "I get an error! How do I solve this?", "Session Info" ], "created": "2018-02-28 23:03:55", "modified": "2023-03-17 14:24:48", "commits": 17 }, { "source": "BioCor_2_advanced.Rmd", "filename": "BioCor_2_advanced.html", "title": "Advanced usage of BioCor", "author": "Lluís Revilla, Juan José Lozano, Pau Sancho-Bru", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Merging similarities", "Assessing a differential study", "Obtaining data", "Selecting differentially expressed genes", "Are differentially expressed genes selected by their functionality?", "Are functionally related the selected differentially expressed genes?", "Influence of the fold change in the functionally similarity of the genes", "Assessing a new pathway", "Merging sources of information", "Comparing with GO similarities", "Session Info" ], "created": "2018-02-28 23:03:55", "modified": "2025-06-22 09:44:46", "commits": 17 } ], "_score": 6.769377326076139, "_indexed": true, "_nocasepkg": "biocor", "_universes": [ "bioc", "llrs" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.37.0", "date": "2026-05-29T06:29:15.000Z", "distro": "noble", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "a7de8d646a24531e46bdbeef504efff83f59a5a237fb7205205bd01ddce4ac37", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" }, { "r": "4.6.0", "os": "linux", "version": "1.37.0", "date": "2026-05-29T06:29:57.000Z", "distro": "noble", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "95d5afd592cd1c3b947b14072a4986e0f831964067d5cacaab17f57d312573d9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" }, { "r": "4.5.3", "os": "mac", "version": "1.37.0", "date": "2026-05-29T06:44:39.000Z", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "99fcbd97e5b349563d70e1a5c9f6f855c869e47b49010fed8c805b36ffdac7ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" }, { "r": "4.6.0", "os": "mac", "version": "1.37.0", "date": "2026-05-29T06:44:34.000Z", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "eea87db6eec9368dfd73c357d613462ebc990fce126a6b98458c28857c3e53d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" }, { "r": "4.6.0", "os": "wasm", "version": "1.37.0", "date": "2026-05-29T06:28:07.000Z", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "197079d84faeab9f5327784951c0f31e0d99dbc0ed63e4fb31b6fb3cd32c0515", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" }, { "r": "4.7.0", "os": "win", "version": "1.37.0", "date": "2026-05-29T06:26:22.000Z", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "9199d3f77517ab34a93af87c82d1f0c7030593f952fe3852fc1f171f9a7f3b55", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" }, { "r": "4.5.3", "os": "win", "version": "1.37.0", "date": "2026-05-29T06:26:29.000Z", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "09421d7a48deb5d383815613453261094ed89c9c32db25bdc92f56741ef363e4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" }, { "r": "4.6.0", "os": "win", "version": "1.37.0", "date": "2026-05-30T05:19:58.000Z", "commit": "0e2f2898499a82cc1022adc31d598b3ca3ec0b61", "fileid": "b53c1615e029ec55b1bc56a1772f33a3ed0e2417028c2c5165da212c0c818bd4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26621461609" } ] }