Package: autonomics
Type: Package
Title: Unified Statistical Modeling of Omics Data
Version: 1.18.0
Authors@R: c(person('Aditya',   'Bhagwat',      email = 'aditya.bhagwat@uni-marburg.de',    role = c('aut', 'cre')), 
             person('Richard',  'Cotton',       email = 'richierocks@gmail.com',            role = c('aut')),
             person('Vanessa',  'Beutgen',      email = 'vanessa.beutgen@uni-marburg.de',   role = c('ctb')),
             person('Witold',   'Szymanski',    email = 'witold.szymanski@uni-marburg.de',  role = c('ctb')),
             person('Shahina',  'Hayat',        email = 'shahina.hayat@hotmail.com',        role = c('ctb')),
             person('Laure',    'Cougnaud',     email = 'laure.cougnaud@openanalytics.eu',  role = c('ctb')), 
             person('Hinrich',  'Goehlmann',    email = 'hinrich@goehlmann.info',           role = c('sad')),
             person('Karsten',  'Suhre',        email = 'kas2049@qatar-med.cornell.edu',    role = c('sad')), 
             person('Johannes', 'Graumann',     email = 'johannes.graumann@uni-marburg.de', role = c('aut', 'sad'))
             )
Description: 
  This package unifies access to Statistal Modeling of Omics Data.
  Across linear modeling engines (lm, lme, lmer, limma, and wilcoxon).
  Across coding systems (treatment, difference, deviation, etc).
  Across model formulae (with/without intercept, random effect, interaction or nesting).
  Across omics platforms (microarray, rnaseq, msproteomics, affinity proteomics, metabolomics).
  Across projection methods (pca, pls, sma, lda, spls, opls).
  Across clustering methods (hclust, pam, cmeans).
  Across survival methods (coxph, survdiff, coin).
  It provides a fast enrichment analysis implementation.
License: GPL-3
Encoding: UTF-8
VignetteBuilder: knitr
biocViews: Software, DataImport, Preprocessing, DimensionReduction,
        PrincipalComponent, Regression, DifferentialExpression,
        GeneSetEnrichment, Transcriptomics, Transcription,
        GeneExpression, RNASeq, Microarray, Proteomics, Metabolomics,
        MassSpectrometry,
BugReports: https://gitlab.uni-marburg.de/fb20/ag-graumann/software/autonomics/issues
RoxygenNote: 7.3.3
Depends: R (>= 4.0)
Imports: abind, arrow, BiocFileCache, BiocGenerics, bit64, cluster,
        codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce,
        ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma,
        lme4, magrittr, matrixStats, methods, MultiAssayExperiment,
        parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors,
        scales, stats, stringi, SummarizedExperiment, survival, tidyr,
        tidyselect, tools, utils, vsn
Suggests: affy, AnnotationDbi, AnnotationHub, apcluster, Biobase,
        BiocManager, BiocStyle, Biostrings, coin, diagram, DBI, e1071,
        ensembldb, GenomicDataCommons, GenomicRanges, GEOquery,
        ggstance, ggridges, ggtext, hgu95av2.db, ICSNP, jsonlite,
        knitr, lmerTest, MASS, mclust, mixOmics, mixtools, mpm, nlme,
        OlinkAnalyze, org.Hs.eg.db, org.Mm.eg.db, patchwork,
        pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite,
        remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer,
        statmod, testthat, UniProt.ws, writexl, XML
git_url: https://git.bioconductor.org/packages/autonomics
git_branch: RELEASE_3_22
git_last_commit: c22fce2
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 02:02:48 UTC; biocbuild
Author: Aditya Bhagwat [aut, cre],
  Richard Cotton [aut],
  Vanessa Beutgen [ctb],
  Witold Szymanski [ctb],
  Shahina Hayat [ctb],
  Laure Cougnaud [ctb],
  Hinrich Goehlmann [sad],
  Karsten Suhre [sad],
  Johannes Graumann [aut, sad]
Maintainer: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Built: R 4.5.1; ; 2025-10-30 09:16:15 UTC; unix
