{ "_id": "6a494d91f6c47c4419499cfd", "Package": "msmsEDA", "Type": "Package", "Title": "Exploratory Data Analysis of LC-MS/MS data by spectral counts", "Version": "1.51.0", "Date": "2014-01-19", "Author": "Josep Gregori, Alex Sanchez, and Josep Villanueva", "Maintainer": "Josep Gregori ", "Description": "Exploratory data analysis to assess the quality of a set\nof LC-MS/MS experiments, and visualize de influence of the\ninvolved factors.", "License": "GPL-2", "Encoding": "latin1", "biocViews": "ImmunoOncology, Software, MassSpectrometry, Proteomics", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev libnetcdf-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:37:58 UTC", "RemoteUrl": "https://github.com/bioc/msmsEDA", "RemoteRef": "HEAD", "RemoteSha": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "NeedsCompilation": "no", "Packaged": { "Date": "2026-07-03 21:46:47 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "msmsEDA_1.51.0.tar.gz", "_fileid": "https://r2.ropensci.org/26b5de5ca15b0edc8b5b7e03d66d0449c886e462140b938b1b6f65176f43e754", "_filesize": 472976, "_sha256": "26b5de5ca15b0edc8b5b7e03d66d0449c886e462140b938b1b6f65176f43e754", "_expires": "2026-10-12T18:14:39.000Z", "_created": "2026-07-03T21:46:47.000Z", "_published": "2026-07-04T18:14:40.994Z", "_bioccheck": { "error": 2, "warning": 3, "note": 11 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920", "_status": "success", "_upstream": "https://github.com/bioc/msmsEDA", "_commit": { "id": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379878 }, "_maintainer": { "name": "Josep Gregori", "email": "josep.gregori@gmail.com", "login": "josepgregori", "description": "", "uuid": 6534561 }, "_distro": "resolute", "_jobs": [ { "job": 85155370557, "time": 197, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "8075231690" }, { "job": 85155370410, "time": 364, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "8075259581" }, { "job": 85155370446, "time": 313, "config": "linux-release-x86_64", "r": "4.6.1", "check": "NOTE", "artifact": "8075251274" }, { "job": 85155370420, "time": 159, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "8075225244" }, { "job": 85155370521, "time": 169, "config": "macos-release-arm64", "r": "4.6.1", "check": "NOTE", "artifact": "8075226889" }, { "job": 85155370296, "time": 313, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "8075198271" }, { "job": 85155370554, "time": 199, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "8075231689" }, { "job": 85155370449, "time": 231, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "8075237845" }, { "job": 85155370737, "time": 212, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "8075234619" }, { "job": 85155370529, "time": 215, "config": "windows-release", "r": "4.6.1", "check": "NOTE", "artifact": "8075234942" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.0.1", "role": "Depends" }, { "package": "MSnbase", "role": "Depends" }, { "package": "MASS", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 2, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.51.0", "bioc": "3.24" }, { "branch": "release", "version": "1.50.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "software", "massspectrometry", "proteomics" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 445, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_mentions": 2, "_searchresults": 4, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/msmsEDA.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "batch.neutralize", "count.stats", "counts.hc", "counts.heatmap", "counts.pca", "disp.estimates", "filter.flags", "gene.table", "norm.counts", "pp.msms.data", "spc.barplots", "spc.boxplots", "spc.densityplots", "spc.scatterplot" ], "_datasets": [ { "name": "msms.dataset", "title": "LC-MS/MS dataset", "object": "msms.dataset", "file": "msms.dataset.rda", "class": [ "MSnSet" ], "fields": [], "table": false, "tojson": false }, { "name": "pnms", "title": "Accessions and gene symbols", "object": "pnms", "file": "pnms.rda", "class": [ "data.frame" ], "fields": [ "Accession", "Proteins" ], "rows": 1160, "table": true, "tojson": true } ], "_help": [ { "page": "msmsEDA-package", "title": "Exploratory Data Analysis of label-free LC-MS/MS spectral counts", "topics": [ "msmsEDA-package", "msmsEDA" ] }, { "page": "batch.neutralize", "title": "Batch effects correction", "topics": [ "batch.neutralize" ] }, { "page": "count.stats", "title": "Summary of statistics of spectral counts by sample in the dataset", "topics": [ "count.stats" ] }, { "page": "counts.hc", "title": "Hierarchical clustering on an spectral counts matrix.", "topics": [ "counts.hc" ] }, { "page": "counts.heatmap", "title": "Heatmap of an spectral counts matrix.", "topics": [ "counts.heatmap" ] }, { "page": "counts.pca", "title": "Principal components analysis of an spectral counts matrix.", "topics": [ "counts.pca" ] }, { "page": "disp.estimates", "title": "Residual dispersion estimates", "topics": [ "disp.estimates" ] }, { "page": "filter.flags", "title": "Flag proteins with a minimum signal and/or sufficient dispersion.", "topics": [ "filter.flags" ] }, { "page": "gene.table", "title": "Gene symbols associated to protein accessions", "topics": [ "gene.table" ] }, { "page": "msms.dataset", "title": "LC-MS/MS dataset", "topics": [ "msms.dataset" ] }, { "page": "norm.counts", "title": "Spectral counts matrix normalization", "topics": [ "norm.counts" ] }, { "page": "pnms", "title": "Accessions and gene symbols", "topics": [ "pnms" ] }, { "page": "pp.msms.data", "title": "Spectral counts matrix pre-processing", "topics": [ "pp.msms.data" ] }, { "page": "spc.barplots", "title": "Set of SpC barplots by sample", "topics": [ "spc.barplots" ] }, { "page": "spc.boxplots", "title": "Set of SpC boxplots by sample", "topics": [ "spc.boxplots" ] }, { "page": "spc.densityplots", "title": "SpC density plots of a SpC matrix", "topics": [ "spc.densityplots" ] }, { "page": "spc.scatterplot", "title": "Scatterplot of SpC means comparing two conditions", "topics": [ "spc.scatterplot" ] } ], "_rundeps": [ "abind", "affy", "affyio", "AnnotationFilter", "askpass", "base64enc", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "biocmake", "BiocManager", "BiocParallel", "bitops", "bslib", "cachem", "caTools", "cli", "clue", "cluster", "codetools", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "digest", "dir.expiry", "doParallel", "dplyr", "evaluate", "farver", "fastmap", "filelock", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gplots", "gtable", "gtools", "highr", "htmltools", "htmlwidgets", "httr", "igraph", "impute", "IRanges", "isoband", "iterators", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "magrittr", "MALDIquant", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "MetaboCoreUtils", "mime", "MsCoreUtils", "MSnbase", "MultiAssayExperiment", "mzID", "mzR", "ncdf4", "openssl", "otel", "pcaMethods", "pillar", "pkgconfig", "plotly", "plyr", "preprocessCore", "promises", "ProtGenerics", "PSMatch", "PTMods", "purrr", "QFeatures", "R6", "rappdirs", "RColorBrewer", "Rcpp", "reshape2", "Rhdf5lib", "rlang", "rmarkdown", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "Seqinfo", "snow", "SparseArray", "Spectra", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "tibble", "tidyr", "tidyselect", "tinytex", "utf8", "vctrs", "viridisLite", "vsn", "withr", "xfun", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "msmsData-Vignette.Rnw", "filename": "msmsData-Vignette.pdf", "title": "msmsEDA: Batch effects detection in LC-MSMS experiments", "engine": "utils::Sweave", "headings": [], "created": "2013-11-01 20:31:28", "modified": "2014-01-19 10:57:55", "commits": 3 } ], "_score": 4.380211241711606, "_indexed": true, "_nocasepkg": "msmseda", "_universes": [ "bioc", "josepgregori" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.51.0", "date": "2026-07-03T21:50:55.000Z", "distro": "resolute", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/c30fa42accf1bebceeabd079799c4e8e324626da3c531b254d79e6c17e19d5c5", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" }, { "r": "4.6.1", "os": "linux", "version": "1.51.0", "date": "2026-07-03T21:50:29.000Z", "distro": "resolute", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/094034d29142d491f8202179383f52fd996216d2d4dbad7243ca8b09450ecdd0", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" }, { "r": "4.5.3", "os": "mac", "version": "1.51.0", "date": "2026-07-03T21:48:53.000Z", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/71ba17be61acc1035ade0fb2a075c7e62bb28481f67e4f415bd80f7d826074db", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" }, { "r": "4.6.1", "os": "mac", "version": "1.51.0", "date": "2026-07-03T21:48:54.000Z", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/be7ff2389097adf6e63510f46542fe14e15c00d2069bcbeb6152dac444fb4285", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" }, { "r": "4.6.0", "os": "wasm", "version": "1.51.0", "date": "2026-07-03T21:50:43.000Z", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/4673547b331e7602ccb6ad1911b3cf8ddef3c6e7bba52354f1fc3871438444fd", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" }, { "r": "4.7.0", "os": "win", "version": "1.51.0", "date": "2026-07-03T21:48:54.000Z", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/313fdcc743c3fe966f7076a975e83fd102e3dda21495be01a29b8bfdaea30800", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" }, { "r": "4.5.3", "os": "win", "version": "1.51.0", "date": "2026-07-03T21:48:44.000Z", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/f4f6bf7f203d69d9b3686c4d2992e967360d20a072ac4ae8e7860e12bf2a0511", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" }, { "r": "4.6.1", "os": "win", "version": "1.51.0", "date": "2026-07-03T21:48:53.000Z", "commit": "9207cea32f6c7b553f0fcbdccf3d01c7b532650b", "fileid": "https://r2.ropensci.org/b5eb6efb3749d2eccc017c09ca2201c2da95b478deb5d6ba54e055fb9face589", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28684567920" } ] }