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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 (3.20)

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). 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.


To view documentation for the version of this package installed in your system, start R and enter:

autonomics_platformaware_analysis HTML R Script
Reference Manual PDF


biocViews DataImport, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, MassSpectrometry, Metabolomics, Microarray, Preprocessing, PrincipalComponent, Proteomics, RNASeq, Regression, Software, Transcription, Transcriptomics
Version 1.13.21
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License GPL-3
Depends R (>= 4.0)
Imports abind, BiocFileCache, BiocGenerics, bit64, cluster, 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, Biobase, BiocManager, BiocStyle, Biostrings, diagram, DBI, e1071, ensembldb, GenomicDataCommons, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, jsonlite, knitr, lme4, lmerTest, MASS, patchwork, 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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Follow Installation instructions to use this package in your R session.

Source Package autonomics_1.13.21.tar.gz
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macOS Binary (x86_64) autonomics_1.13.21.tgz
macOS Binary (arm64) autonomics_1.13.21.tgz
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