{ "_id": "6a10191dacfb0bcc41c85d26", "Package": "proteoDeconv", "Title": "Enabling Cell-Type Deconvolution of Proteomics Data", "Version": "0.1.2", "Authors@R": "person(\"Måns\", \"Zamore\", email = \"mans.zamore@immun.lth.se\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8108-1097\"))", "Description": "Tools for deconvoluting proteomics data to identify and\nquantify cell types (e.g., immune cell types) in complex\nbiological samples.", "License": "MIT + file LICENSE", "URL": "https://github.com/ComputationalProteomics/proteoDeconv,\nhttps://computationalproteomics.github.io/proteoDeconv/", "BugReports": "https://github.com/ComputationalProteomics/proteoDeconv/issues", "Remotes": [ "WangLab-MSSM/BayesDeBulk/BayesDeBulk", "GfellerLab/EPIC", "omnideconv/SimBu" ], "Config/testthat/edition": "3", "Encoding": "UTF-8", "SystemRequirements": "Docker", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev make libicu-dev libpng-dev libxml2-dev\npython3 libx11-dev zlib1g-dev", "Repository": "https://computationalproteomics.r-universe.dev", "Date/Publication": "2026-03-23 18:15:18 UTC", "RemoteUrl": "https://github.com/ComputationalProteomics/proteoDeconv", "RemoteRef": "HEAD", "RemoteSha": "2379af2771e2145db665bba39dd3d88c85b96aa8", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-22 08:46:41 UTC", "User": "root" }, "Author": "Måns Zamore [aut, cre] (ORCID: )", "Maintainer": "Måns Zamore ", "MD5sum": "78e9a078f6e5764a670e565df80619bc", "_user": "computationalproteomics", "_type": "src", "_file": "proteoDeconv_0.1.2.tar.gz", "_fileid": "d3885a62017cf81c0e4e54351daaa11574524526ff2bc779484fce590abe7266", "_filesize": 1470753, "_sha256": "d3885a62017cf81c0e4e54351daaa11574524526ff2bc779484fce590abe7266", "_created": "2026-05-22T08:46:41.000Z", "_published": "2026-05-22T08:51:41.101Z", "_distro": "noble", "_jobs": [ { "job": 77346765805, "time": 219, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7156554987" }, { "job": 77346765799, "time": 221, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7156555944" }, { "job": 77346765795, "time": 222, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7156547350" }, { "job": 77346765806, "time": 259, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7156554265" }, { "job": 77346017435, "time": 301, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7156488654" }, { "job": 77346765818, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156544807" }, { "job": 77346765817, "time": 172, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7156541155" }, { "job": 77346765826, "time": 165, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7156539048" }, { "job": 77346765832, "time": 155, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7156536229" } ], "_buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/ComputationalProteomics/proteoDeconv", "_commit": { "id": "2379af2771e2145db665bba39dd3d88c85b96aa8", "author": "Måns Zamore <55241+manszamore@users.noreply.github.com>", "committer": "GitHub ", "message": "Merge pull request #3 from ComputationalProteomics/dev\n\nfix tests", "time": 1774289718 }, "_maintainer": { "name": "Måns Zamore", "email": "mans.zamore@immun.lth.se", "login": "manszamore", "orcid": "0000-0002-8108-1097", "description": "PhD student in computational proteomics", "uuid": 55241 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "dplyr", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "HGNChelper", "role": "Imports" }, { "package": "impute", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "MsCoreUtils", "role": "Imports" }, { "package": "readr", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "SimBu", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "stringr", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "tibble", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "tidyselect", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BayesDeBulk", "role": "Suggests" }, { "package": "EPIC", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" } ], "_owner": "computationalproteomics", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-29", "n": 3 }, { "week": "2025-37", "n": 1 }, { "week": "2026-13", "n": 2 } ], "_tags": [], "_stars": 8, "_contributors": [ { "user": "manszamore", "count": 73, "uuid": 55241 } ], "_userbio": { "uuid": 31468468, "type": "organization", "name": "Computational Proteomics", "description": "Computational Proteomics at department of Immunotechnology, Lund University" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/proteoDeconv" }, "_devurl": "https://github.com/computationalproteomics/proteodeconv", "_pkgdown": "https://computationalproteomics.github.io/proteoDeconv/", "_searchresults": 6, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/proteoDeconv.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_cranurl": false, "_exports": [ "convert_to_tpm", "create_phenoclasses", "create_signature_matrix", "deconvolute", "deconvolute_bayesdebulk", "deconvolute_cibersort", "deconvolute_cibersortx", "deconvolute_epic", "extract_identifiers", "handle_duplicates", "handle_missing_values", "handle_scaling", "map_cell_groups", "simulate_data", "unlog2_data", "update_gene_symbols" ], "_help": [ { "page": "convert_to_tpm", "title": "Convert protein abundance data to TPM-like normalization", "topics": [ "convert_to_tpm" ] }, { "page": "create_phenoclasses", "title": "Create phenoclasses matrix for cell type deconvolution", "topics": [ "create_phenoclasses" ] }, { "page": "create_signature_matrix", "title": "Create signature matrix using CIBERSORTx", "topics": [ "create_signature_matrix" ] }, { "page": "deconvolute", "title": "Deconvolute protein data using multiple algorithms", "topics": [ "deconvolute" ] }, { "page": "deconvolute_bayesdebulk", "title": "Deconvolute bulk proteome data using BayesDeBulk", "topics": [ "deconvolute_bayesdebulk" ] }, { "page": "deconvolute_cibersort", "title": "Deconvolute mixture data using CIBERSORT", "topics": [ "deconvolute_cibersort" ] }, { "page": "deconvolute_cibersortx", "title": "Deconvolute using CIBERSORTx Docker image", "topics": [ "deconvolute_cibersortx" ] }, { "page": "deconvolute_epic", "title": "Deconvolute bulk data using EPIC", "topics": [ "deconvolute_epic" ] }, { "page": "extract_identifiers", "title": "Extract primary identifiers from e.g. protein groups", "topics": [ "extract_identifiers" ] }, { "page": "handle_duplicates", "title": "Handle duplicate identifiers in an expression matrix", "topics": [ "handle_duplicates" ] }, { "page": "handle_missing_values", "title": "Handle missing values", "topics": [ "handle_missing_values" ] }, { "page": "handle_scaling", "title": "Handle scaling of protein abundance data", "topics": [ "handle_scaling" ] }, { "page": "map_cell_groups", "title": "Map column names to cell type groups using patterns", "topics": [ "map_cell_groups" ] }, { "page": "simulate_data", "title": "Simulate artifical mixtures from bulk proteome measurements", "topics": [ "simulate_data" ] }, { "page": "unlog2_data", "title": "Convert data from log2 scale to linear scale", "topics": [ "unlog2_data" ] }, { "page": "update_gene_symbols", "title": "Update gene symbols in a matrix to approved HGNC nomenclature", "topics": [ "update_gene_symbols" ] } ], "_readme": "https://github.com/ComputationalProteomics/proteoDeconv/raw/HEAD/README.md", "_rundeps": [ "abind", "ade4", "ape", "basilisk", "BH", "Biobase", "BiocGenerics", "BiocParallel", "biomformat", "Biostrings", "bit", "bit64", "bitops", "cli", "clipr", "clue", "cluster", "codetools", "cpp11", "crayon", "data.table", "DelayedArray", "digest", "dir.expiry", "dplyr", "farver", "filelock", "foreach", "formatR", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "here", "HGNChelper", "hms", "igraph", "impute", "IRanges", "isoband", "iterators", "jsonlite", "labeling", "lambda.r", "lattice", "lifecycle", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mgcv", "MsCoreUtils", "multtest", "nlme", "permute", "phyloseq", "pillar", "pixmap", "pkgconfig", "plyr", "png", "prettyunits", "progress", "proxyC", "purrr", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppTOML", "RCurl", "readr", "reshape2", "reticulate", "rlang", "rprojroot", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SimBu", "snow", "sp", "SparseArray", "sparseMatrixStats", "splitstackshape", "stringi", "stringr", "SummarizedExperiment", "survival", "tibble", "tidyr", "tidyselect", "tzdb", "utf8", "vctrs", "vegan", "viridisLite", "vroom", "withr", "XVector" ], "_vignettes": [ { "source": "proteoDeconv.Rmd", "filename": "proteoDeconv.html", "title": "Introduction to proteoDeconv", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Loading required packages", "Example data overview", "Data preprocessing", "Preprocessing options", "Creating a signature matrix", "Performing deconvolution", "Available deconvolution algorithms", "Formatting and visualizing results", "Conclusion", "References" ], "created": "2025-03-06 18:43:44", "modified": "2025-03-07 05:25:38", "commits": 5 } ], "_score": 4.079181246047625, "_indexed": true, "_nocasepkg": "proteodeconv", "_universes": [ "computationalproteomics", "manszamore" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.2", "date": "2026-05-22T08:49:54.000Z", "distro": "noble", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "db8cfe7a1ad34e75896e5874d0aabdc9427b4682dbd613e1fdfa0b53c591c33d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" }, { "r": "4.6.0", "os": "linux", "version": "0.1.2", "date": "2026-05-22T08:50:00.000Z", "distro": "noble", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "1c9eae2e42a5d3a0c51fcda0a22d4c9662da7c5de2878b0cf279659be486bfc9", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" }, { "r": "4.5.3", "os": "mac", "version": "0.1.2", "date": "2026-05-22T08:49:44.000Z", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "2b268fb6f80c40f3800dd13351b758e23bb4c04d5e9982c82ad1624fdb2d9e91", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" }, { "r": "4.6.0", "os": "mac", "version": "0.1.2", "date": "2026-05-22T08:49:49.000Z", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "a73d2801d53586721f3089bac6172bea78ddc2c38e3aeeb50ee394d75a684d26", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.2", "date": "2026-05-22T08:50:04.000Z", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "229348334e3900f77a0d4e355b16cd6fc125cefad700bad21411e588bd94e01e", "status": "success", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" }, { "r": "4.7.0", "os": "win", "version": "0.1.2", "date": "2026-05-22T08:49:00.000Z", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "ef5fb0884179d4b8942a3b73852b81b0263c9a018dec0b07b61ca76dcfbdc513", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" }, { "r": "4.5.3", "os": "win", "version": "0.1.2", "date": "2026-05-22T08:48:58.000Z", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "ee6b553fa3490f838da6ba04244d7ac666ea877010ec4dfc0d5e98d1370df2c6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" }, { "r": "4.6.0", "os": "win", "version": "0.1.2", "date": "2026-05-22T08:48:45.000Z", "commit": "2379af2771e2145db665bba39dd3d88c85b96aa8", "fileid": "57c29b1d7576dab53851b46d0aa7c5b21a072e425ed5962b68fd9ad2871b7634", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/computationalproteomics/actions/runs/26277719644" } ] }