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This is the development version of autonomics; for the stable release version, see autonomics.

Unified statistal Modeling of Omics Data

Bioconductor version: Development (3.19)

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). It provides a fast enrichment analysis implementation. And an intuitive contrastogram visualisation to summarize contrast effects in complex designs.

Author: Aditya Bhagwat [aut, cre], Richard Cotton [aut], Shahina Hayat [aut], Laure Cougnaud [ctb], Witold Szymanski [ctb], Vanessa Beutgen [ctb], Willem Ligtenberg [sad], Hinrich Goehlmann [sad], Karsten Suhre [sad], Johannes Graumann [aut, sad, rth]

Maintainer: Aditya Bhagwat <aditya.bhagwat at>

Citation (from within R, enter citation("autonomics")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews DataImport, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, MassSpectrometry, Metabolomics, Microarray, Preprocessing, PrincipalComponent, Proteomics, RNASeq, Regression, Software, Transcription, Transcriptomics
Version 1.11.102
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.0)
Imports abind, BiocFileCache, BiocGenerics, bit64, codingMatrices, colorspace, data.table, dplyr, edgeR, ggforce, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, RColorBrewer, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tidyselect, tools, utils, vsn
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Suggests affy, AnnotationDbi, AnnotationHub, apcluster, BiocManager, BiocStyle, Biostrings, diagram, DBI, ensembldb, fpc, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, OlinkAnalyze,,, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, survival, survminer, testthat,, writexl, XML
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