{ "_id": "6a197bf7acfb0bcc41df60b1", "Package": "glmmSeq", "Title": "General Linear Mixed Models for Gene-Level Differential\nExpression", "Version": "0.5.7", "Authors@R": "c(person(given = \"Myles\",family = \"Lewis\",\nrole = c(\"aut\", \"cre\"),\nemail = \"myles.lewis@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0001-9365-5345\")),\nperson(given = \"Katriona\",family = \"Goldmann\",\nrole = c(\"aut\"),\nemail = \"k.goldmann@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0002-9073-6323\")),\nperson(given = \"Elisabetta\",family = \"Sciacca\",\nrole = c(\"aut\"),\nemail = \"e.sciacca@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0001-7525-1558\")),\nperson(given = \"Cankut\",family = \"Cubuk\",\nrole = c(\"ctb\"),\nemail = \"c.cubuk@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0003-4646-0849\")),\nperson(given = \"Anna\", family = \"Surace\",\nrole = c(\"ctb\"),\nemail = \"a.surace@qmul.ac.uk\",\ncomment = c(ORCID = \"0000-0001-9589-3005\")))", "Description": "Using mixed effects models to analyse longitudinal gene\nexpression can highlight differences between sample groups over\ntime. The most widely used differential gene expression tools\nare unable to fit linear mixed effect models, and are less\noptimal for analysing longitudinal data. This package provides\nnegative binomial and Gaussian mixed effects models to fit gene\nexpression and other biological data across repeated samples.\nThis is particularly useful for investigating changes in\nRNA-Sequencing gene expression between groups of individuals\nover time, as described in: Rivellese, F., Surace, A. E.,\nGoldmann, K., Sciacca, E., Cubuk, C., Giorli, G., ... Lewis, M.\nJ., & Pitzalis, C. (2022) Nature medicine\n.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "biocViews": "", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Language": "en-gb", "URL": "https://myles-lewis.github.io/glmmSeq/,\nhttps://github.com/myles-lewis/glmmSeq", "BugReports": "https://github.com/myles-lewis/glmmSeq/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev make libharfbuzz-dev libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev", "Repository": "https://myles-lewis.r-universe.dev", "Date/Publication": "2025-10-01 19:55:13 UTC", "RemoteUrl": "https://github.com/myles-lewis/glmmseq", "RemoteRef": "HEAD", "RemoteSha": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-29 10:30:04 UTC", "User": "root" }, "Author": "Myles Lewis [aut, cre] (ORCID: ),\nKatriona Goldmann [aut] (ORCID:\n),\nElisabetta Sciacca [aut] (ORCID:\n),\nCankut Cubuk [ctb] (ORCID: ),\nAnna Surace [ctb] (ORCID: )", "Maintainer": "Myles Lewis ", "MD5sum": "206558edbd78dea8cb16d4a0d00987a2", "_user": "myles-lewis", "_type": "src", "_file": "glmmSeq_0.5.7.tar.gz", "_fileid": "4cf91558678bdcfa988e62c5ed110c2ce35f8b4812591e21909a01488ee3dc0f", "_filesize": 1484240, "_sha256": "4cf91558678bdcfa988e62c5ed110c2ce35f8b4812591e21909a01488ee3dc0f", "_created": "2026-05-29T10:30:04.000Z", "_published": "2026-05-29T11:43:51.024Z", "_distro": "noble", "_jobs": [ { "job": 78483686670, "time": 228, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7288678301" }, { "job": 78483686657, "time": 210, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7288673615" }, { "job": 78483686737, "time": 164, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7289848699" }, { "job": 78483686755, "time": 111, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7289836935" }, { "job": 78482964327, "time": 302, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7288611833" }, { "job": 78483686661, "time": 162, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7288659669" }, { "job": 78483686707, "time": 198, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7288670134" }, { "job": 78483686698, "time": 131, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7288651119" }, { "job": 78483686758, "time": 142, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7288654390" } ], "_buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/myles-lewis/glmmseq", "_commit": { "id": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "author": "Elisabetta <70027703+elisabettasciacca@users.noreply.github.com>", "committer": "Elisabetta <70027703+elisabettasciacca@users.noreply.github.com>", "message": "Update CRAN-SUBMISSION\n", "time": 1759348513 }, "_maintainer": { "name": "Myles Lewis", "email": "myles.lewis@qmul.ac.uk", "login": "myles-lewis", "description": "", "uuid": 24961656, "orcid": "0000-0001-9365-5345" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "car", "role": "Imports" }, { "package": "emmeans", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "glmmTMB", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "MASS", "role": "Imports" }, { "package": "lme4", "role": "Imports" }, { "package": "lmerTest", "role": "Imports" }, { "package": "kableExtra", "role": "Imports" }, { "package": "mcprogress", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "plotly", "role": "Imports" }, { "package": "qvalue", "role": "Imports" }, { "package": "pbapply", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "edgeR", "role": "Suggests" } ], "_owner": "myles-lewis", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-39", "n": 3 }, { "week": "2025-40", "n": 6 } ], "_tags": [], "_topics": [ "bioinformatics", "differential-gene-expression", "gene-expression", "glmm", "mixed-models", "transcriptomics" ], "_stars": 25, "_contributors": [ { "user": "myles-lewis", "count": 200, "uuid": 24961656 }, { "user": "katrionagoldmann", "count": 19, "uuid": 25952322 }, { "user": "elisabettasciacca", "count": 14, "uuid": 70027703 }, { "user": "zktuong", "count": 9, "uuid": 26215587 } ], "_userbio": { "uuid": 24961656, "type": "user", "name": "Myles Lewis" }, "_downloads": { "count": 343, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/glmmSeq" }, "_devurl": "https://github.com/myles-lewis/glmmseq", "_pkgdown": "https://myles-lewis.github.io/glmmSeq/", "_searchresults": 49, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/glmmSeq.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/myles-lewis/glmmseq", "_realowner": "myles-lewis", "_cranurl": true, "_releases": [ { "version": "0.0.1", "date": "2021-03-11" }, { "version": "0.1.0", "date": "2021-03-30" }, { "version": "0.2.0", "date": "2022-07-11" }, { "version": "0.4.0", "date": "2022-08-12" }, { "version": "0.5.1", "date": "2022-09-12" }, { "version": "0.5.5", "date": "2022-10-08" }, { "version": "0.5.7", "date": "2025-10-03" } ], "_exports": [ "fcPlot", "ggmodelPlot", "glmmQvals", "glmmRefit", "glmmSeq", "lmmSeq", "maPlot", "modelPlot" ], "_datasets": [ { "name": "metadata", "title": "Minimal metadata from PEAC", "object": "PEAC_minimal_load", "class": [ "data.frame" ], "fields": [ "PATID", "Timepoint", "EULAR_6m" ], "rows": 123, "table": true, "tojson": true }, { "name": "tpm", "title": "TPM count data from PEAC", "object": "PEAC_minimal_load", "class": [ "matrix", "array" ], "fields": [ "S9001", "S9002", "S9003", "S9004", "S9006", "S9007", "S9008", "S9009", "S9010", "S9011", "S9012", "S9013", "S9014", "S9016", "S9017", "S9018", "S9019", "S9020", "S9021", "S9023", "S9025", "S9029", "S9034", "S9035", "S9036", "S9038", "S9039", "S9040", "S9042", "S9043", "S9044", "S9045", "S9047", "S9048", "S9049", "S9052", "S9053", "S9054", "S9056", "S9059", "S9060", "S9063", "S9065", "S9066", "S9067", "S9068", "S9069", "S9070", "S9072", "S9073", "S9074", "S9075", "S9076", "S9077", "S9078", "S9079", "S9080", "S9081", "S9083", "S9084", "S9085", "S9086", "S9087", "S9088", "S9089", "S9090", "S9091", "S9092", "S9093", "S9094", "S9095", "S9096", "S9097", "S9098", "S9099", "S9100", "S9101", "S9102", "S9103", "S9104", "S9105", "S9106", "S9107", "S9108", "S9109", "S9110", "S9111", "S9112", "S9113", "S9114", "S9115", "S9116", "S9117", "S9119", "S9120", "S9121", "S9122", "S9123", "S9124", "S9125", "S9127", "S9128", "S9129", "S9130", "S9131", "S9132", "S9133", "S9134", "S9135", "S9136", "S9137", "S9138", "S9139", "S9140", "S9141", "S9142", "S9143", "S9144", "S9145", "S9146", "S9147", "S9148", "S9149" ], "rows": 50, "table": true, "tojson": true } ], "_help": [ { "page": "fcPlot", "title": "Plotly or ggplot fold change plots", "topics": [ "fcPlot" ] }, { "page": "ggmodelPlot", "title": "Mixed model effects plot using ggplot2", "topics": [ "ggmodelPlot" ] }, { "page": "glmmQvals", "title": "Glmm Sequencing qvalues", "topics": [ "glmmQvals" ] }, { "page": "glmmRefit", "title": "Refit mixed effects model", "topics": [ "glmmRefit", "glmmRefit.GlmmSeq", "glmmRefit.lmmSeq" ] }, { "page": "glmmSeq", "title": "GLMM with negative binomial distribution for sequencing count data", "topics": [ "glmmSeq" ] }, { "page": "GlmmSeq-class", "title": "An S4 class to define the glmmSeq output", "topics": [ "GlmmSeq-class" ] }, { "page": "lmmSeq", "title": "Linear mixed models for data matrix", "topics": [ "lmmSeq" ] }, { "page": "lmmSeq-class", "title": "An S4 class to define the lmmSeq output", "topics": [ "lmmSeq-class" ] }, { "page": "maPlot", "title": "MA plots", "topics": [ "maPlot" ] }, { "page": "metadata", "title": "Minimal metadata from PEAC", "topics": [ "metadata" ] }, { "page": "modelPlot", "title": "Mixed model effects plot", "topics": [ "modelPlot" ] }, { "page": "summary.lmmSeq", "title": "Summarise a 'glmmSeq'/'lmmSeq' object", "topics": [ "summary.GlmmSeq", "summary.lmmSeq" ] }, { "page": "tpm", "title": "TPM count data from PEAC", "topics": [ "tpm" ] } ], "_pkglogo": "https://github.com/myles-lewis/glmmseq/raw/HEAD/logo.png", "_readme": "https://github.com/myles-lewis/glmmseq/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "backports", "base64enc", "boot", "broom", "bslib", "cachem", "car", "carData", "cli", "colorspace", "corrplot", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "Deriv", "digest", "doBy", "dplyr", "emmeans", "estimability", "evaluate", "farver", "fastmap", "fontawesome", "forecast", "Formula", "fracdiff", "fs", "generics", "ggplot2", "ggpubr", "ggrepel", "ggsci", "ggsignif", "glmmTMB", "glue", "gridExtra", "gtable", "highr", "htmltools", "htmlwidgets", "httr", "isoband", "jquerylib", "jsonlite", "kableExtra", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "lme4", "lmerTest", "lmtest", "magrittr", "MASS", "Matrix", "MatrixModels", "mcprogress", "memoise", "mgcv", "microbenchmark", "mime", "minqa", "modelr", "mvtnorm", "nlme", "nloptr", "nnet", "numDeriv", "openssl", "otel", "pbapply", "pbkrtest", "pillar", "pkgconfig", "plotly", "plyr", "polynom", "promises", "purrr", "quantreg", "qvalue", "R6", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppArmadillo", "RcppEigen", "Rdpack", "reformulas", "reshape2", "rlang", "rmarkdown", "rstatix", "rstudioapi", "S7", "sandwich", "sass", "scales", "SparseM", "stringi", "stringr", "survival", "svglite", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "timeDate", "tinytex", "TMB", "urca", "utf8", "vctrs", "viridisLite", "withr", "xfun", "xml2", "yaml", "zoo" ], "_vignettes": [ { "source": "glmmSeq.rmd", "filename": "glmmSeq.html", "title": "glmmSeq", "author": "Myles Lewis, Katriona Goldmann, Elisabetta Sciacca, Cankut Cubuk, Anna Surace", "engine": "knitr::rmarkdown", "headings": [ "glmmSeq", "Installing from CRAN", "Installing from Github", "Installing Locally", "Overview", "Metadata", "Count data", "Dispersion", "Size Factors", "Fitting Models", "Outputs", "Q-values", "glmmTMB models", "Gaussian mixed effects models", "Hypothesis testing", "Extracting individual Genes", "Refitting a different model", "Model Plots", "Fold change plots", "MA plots", "Troubleshooting", "Citing glmmSeq", "References" ], "created": "2020-08-17 13:43:35", "modified": "2025-09-26 13:56:46", "commits": 31 } ], "_score": 6.565257343420214, "_indexed": true, "_nocasepkg": "glmmseq", "_universes": [ "myles-lewis" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.5.7", "date": "2026-05-29T10:33:24.000Z", "distro": "noble", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "1606eaaeeea274cd1084907c4302b8fb08a55962f3e0f0259f13db016a93f9ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" }, { "r": "4.6.0", "os": "linux", "version": "0.5.7", "date": "2026-05-29T10:33:11.000Z", "distro": "noble", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "9e0b45cf0eceabe0cc7e4a5247a551668dabbbd60a7bf7c1f4e8d7ee60dbc9a3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" }, { "r": "4.5.3", "os": "mac", "version": "0.5.7", "date": "2026-05-29T11:42:49.000Z", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "8a49ddd695f2145978fd125898d72146a3188ccb6de8a0ecf1c73601736d8230", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" }, { "r": "4.6.0", "os": "mac", "version": "0.5.7", "date": "2026-05-29T11:42:11.000Z", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "cb3e12e80e63542609b22b501315d03c37a200fa612ed6648c99329c020d2726", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" }, { "r": "4.6.0", "os": "wasm", "version": "0.5.7", "date": "2026-05-29T10:33:16.000Z", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "03e8baa5406d99a38d300d538b9899dc6bbea8cc65c37b1e05c6e0424ec48f67", "status": "success", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" }, { "r": "4.7.0", "os": "win", "version": "0.5.7", "date": "2026-05-29T10:32:32.000Z", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "cc742dba157a51d94e663bf44133b03c4a469a6f9d4784ca44000f896a288789", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" }, { "r": "4.5.3", "os": "win", "version": "0.5.7", "date": "2026-05-29T10:31:44.000Z", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "d72a52f8ab0ccf822d026c58a16f1a0d1ff30265bb28883fdf612fa5704e3845", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" }, { "r": "4.6.0", "os": "win", "version": "0.5.7", "date": "2026-05-29T10:31:52.000Z", "commit": "8e3e49c5f9db2d7fd90d2dc30849197a30aad6d7", "fileid": "154807f3d9f85a887368306808562ddd840dee1f3c90a6a08dd98a4421793897", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/myles-lewis/actions/runs/26632004213" } ] }