{ "_id": "6a195257acfb0bcc41ddfe76", "Package": "nempi", "Type": "Package", "Title": "Inferring unobserved perturbations from gene expression data", "Version": "1.20.0", "Authors@R": "person(\"Martin\", \"Pirkl\", \nemail = \"martinpirkl@yahoo.de\",\nrole = c(\"aut\", \"cre\"))", "Description": "Takes as input an incomplete perturbation profile and\ndifferential gene expression in log odds and infers unobserved\nperturbations and augments observed ones. The inference is done\nby iteratively inferring a network from the perturbations and\ninferring perturbations from the network. The network inference\nis done by Nested Effects Models.", "License": "GPL-3", "Encoding": "UTF-8", "biocViews": "Software, GeneExpression, DifferentialExpression,\nDifferentialMethylation, GeneSignaling, Pathways, Network,\nClassification, NeuralNetwork, NetworkInference, ATACSeq,\nDNASeq, RNASeq, PooledScreens, CRISPR, SingleCell,\nSystemsBiology", "VignetteBuilder": "knitr", "BugReports": "https://github.com/cbg-ethz/nempi/issues", "URL": "https://github.com/cbg-ethz/nempi/", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "libglpk-dev libjpeg-dev libpng-dev libxml2-dev\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:54:36 UTC", "RemoteUrl": "https://github.com/bioc/nempi", "RemoteRef": "RELEASE_3_23", "RemoteSha": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 07:38:09 UTC", "User": "root" }, "Author": "Martin Pirkl [aut, cre]", "Maintainer": "Martin Pirkl ", "MD5sum": "e3b0b344620ede40fd149fea71e08f35", "_user": "bioc-release", "_type": "src", "_file": "nempi_1.20.0.tar.gz", "_fileid": "08296ec5915f86f09a2d41f901603974ba60a758f7012334648d9ffe3fb3283c", "_filesize": 491817, "_sha256": "08296ec5915f86f09a2d41f901603974ba60a758f7012334648d9ffe3fb3283c", "_created": "2026-05-29T07:38:09.000Z", "_published": "2026-05-29T08:46:15.768Z", "_jobs": [ { "job": 78458619035, "time": 190, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7285628044" }, { "job": 78458618920, "time": 271, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7285650993" }, { "job": 78458618927, "time": 323, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7285665893" }, { "job": 78458618947, "time": 148, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7286734086" }, { "job": 78458618903, "time": 128, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7286723276" }, { "job": 78457854236, "time": 327, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7285570400" }, { "job": 78458618905, "time": 196, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7285629553" }, { "job": 78458618928, "time": 176, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7285623976" }, { "job": 78458618933, "time": 172, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7285622370" }, { "job": 78458619015, "time": 239, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7285643568" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/nempi", "_commit": { "id": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777380876 }, "_maintainer": { "name": "Martin Pirkl", "email": "martinpirkl@yahoo.de", "login": "martinfxp", "description": "", "uuid": 12323002 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "mnem", "role": "Depends" }, { "package": "e1071", "role": "Imports" }, { "package": "nnet", "role": "Imports" }, { "package": "randomForest", "role": "Imports" }, { "package": "naturalsort", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "epiNEM", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocGenerics", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "RUnit", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.21.0", "bioc": "3.24" }, { "branch": "release", "version": "1.20.0", "bioc": "3.23" } ], "_topics": [ "software", "geneexpression", "differentialexpression", "differentialmethylation", "genesignaling", "pathways", "network", "classification", "neuralnetwork", "networkinference", "atacseq", "dnaseq", "rnaseq", "pooledscreens", "crispr", "singlecell", "systemsbiology" ], "_stars": 2, "_contributors": [ { "user": "jwokaty", "count": 10, "uuid": 1744257 }, { "user": "martinfxp", "count": 7, "uuid": 12323002 }, { "user": "nturaga", "count": 6, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 330, "source": "https://www.bioconductor.org/packages/stats/bioc/nempi" }, "_devurl": "https://github.com/cbg-ethz/nempi", "_searchresults": 2, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/nempi.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/cbg-ethz/nempi", "_realowner": "bioc", "_cranurl": false, "_exports": [ "classpi", "nempi", "nempibs", "pifit" ], "_help": [ { "page": "classpi", "title": "Classification", "topics": [ "classpi" ] }, { "page": "nempi", "title": "Main function for NEM based perturbation imputation.", "topics": [ "nempi" ] }, { "page": "nempibs", "title": "Bootstrapping function", "topics": [ "nempibs" ] }, { "page": "pifit", "title": "Accuracy computation", "topics": [ "pifit" ] }, { "page": "plot.nempi", "title": "Plotting nempi", "topics": [ "plot.nempi" ] }, { "page": "plotConvergence.nempi", "title": "Plot convergence of EM", "topics": [ "plotConvergence.nempi" ] } ], "_readme": "https://github.com/bioc/nempi/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "amap", "apcluster", "bdsmatrix", "BH", "BiocGenerics", "BiocManager", "BoolNet", "BoutrosLab.plotting.general", "class", "cli", "clue", "cluster", "colorspace", "corpcor", "cpp11", "data.table", "deldir", "DEoptimR", "diptest", "e1071", "ellipse", "epiNEM", "farver", "fastcluster", "fastICA", "flexclust", "flexmix", "fpc", "gdata", "generics", "ggdendro", "ggm", "ggplot2", "glue", "gmodels", "graph", "gridExtra", "gtable", "gtools", "hexbin", "igraph", "infotheo", "interp", "isoband", "jpeg", "kernlab", "labeling", "latex2exp", "lattice", "latticeExtra", "lifecycle", "limma", "Linnorm", "lmtest", "magrittr", "MASS", "Matrix", "matrixStats", "mclust", "mgcv", "minet", "mnem", "modeltools", "naturalsort", "nlme", "nnet", "pcalg", "permute", "pkgconfig", "png", "prabclus", "proxy", "R6", "randomForest", "RBGL", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rgraphviz", "rlang", "robustbase", "Rtsne", "S7", "scales", "sfsmisc", "snow", "snowfall", "statmod", "tsne", "vcd", "vctrs", "vegan", "viridisLite", "wesanderson", "withr", "XML", "zoo" ], "_vignettes": [ { "source": "nempi.Rmd", "filename": "nempi.html", "title": "| Nested Effects Models-based perturbation inference: | Inference of unobserved perturbations from gene expression profiles.", "author": "Martin Pirkl, Niko Beerenwinkel", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation and loading", "Small example", "Data simulation", "Perturbation inference", "Prior matrix", "Final perturbation matrix", "Session information", "References:" ], "created": "2019-09-02 12:35:02", "modified": "2022-09-23 07:02:46", "commits": 7 } ], "_score": 4.6020599913279625, "_indexed": false, "_nocasepkg": "nempi", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/nempi", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.20.0", "date": "2026-05-29T07:41:25.000Z", "distro": "noble", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "9c611e064b2a673f26f8ffe5c1a33edf6fcf536ea6ee028cfc6554a2b305afbd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" }, { "r": "4.6.0", "os": "linux", "version": "1.20.0", "date": "2026-05-29T07:42:16.000Z", "distro": "noble", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "ec68c1076f05543d453d4905bcd38eb8a36fd8471858e46358b9192e3f2a3a84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" }, { "r": "4.5.3", "os": "mac", "version": "1.20.0", "date": "2026-05-29T08:44:55.000Z", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "32a733782a557af28edeee28ff37ce13bd3086e4f3cf6461eab79b4a2fa543f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" }, { "r": "4.6.0", "os": "mac", "version": "1.20.0", "date": "2026-05-29T08:44:27.000Z", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "cbc70ab46a4e9c4f0cad136c3f182d38662da389b5a59b65e847b6e16b2c1459", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" }, { "r": "4.6.0", "os": "wasm", "version": "1.20.0", "date": "2026-05-29T07:41:54.000Z", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "1fc7c6fa8683a34c8f4c7e0b908be839b64dece723332d2519e027a16d3297f4", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" }, { "r": "4.7.0", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:39:54.000Z", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "0f1bf2c22dc89111465943bc31b0232cd2ede6786969796502152e130b3b2e84", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" }, { "r": "4.5.3", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:39:52.000Z", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "cf9ab77b692158dcebcc3722b7fef2de05da713928f84f6ac34584249bd94014", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" }, { "r": "4.6.0", "os": "win", "version": "1.20.0", "date": "2026-05-29T07:41:02.000Z", "commit": "6c373eae74db4e2668c72f5e602ebc877e6ef447", "fileid": "00512412aea1ad07f4c9ba048973dd1b25ea4e9f93b93bebb7890f88b088072f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624478434" } ] }