autonomics

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see autonomics.

Unified statistal Modeling of Omics Data

Bioconductor version: 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 uni-marburg.de>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("autonomics")

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

Documentation

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

browseVignettes("autonomics")

autonomics_platformaware_analysis HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DifferentialExpression, DimensionReduction, GeneExpression, GeneSetEnrichment, MassSpectrometry, Metabolomics, Microarray, Preprocessing, PrincipalComponent, Proteomics, RNASeq, Regression, Software, Transcription, Transcriptomics

Version 1.12.1

In Bioconductor since BioC 3.13 (R-4.1) (3.5 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

System Requirements

URL https://github.com/bhagwataditya/autonomics

Bug Reports https://github.com/bhagwataditya/autonomics

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, org.Hs.eg.db, org.Mm.eg.db, pcaMethods, pheatmap, progeny, propagate, RCurl, RSQLite, remotes, rmarkdown, ropls, Rsubread, readODS, rtracklayer, statmod, survival, survminer, testthat, UniProt.ws, writexl, XML

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package autonomics_1.12.1.tar.gz

Windows Binary (x86_64) autonomics_1.12.1.zip

macOS Binary (x86_64) autonomics_1.12.1.tgz

macOS Binary (arm64) autonomics_1.12.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/autonomics

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/autonomics

Bioc Package Browser https://code.bioconductor.org/browse/autonomics/

Package Short Url https://bioconductor.org/packages/autonomics/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.19 Source Archive