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

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
See More
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
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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 [email protected]: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