autonomics

DOI: 10.18129/B9.bioc.autonomics    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see autonomics.

Generifying and intuifying cross-platform omics analysis

Bioconductor version: 3.13

This package offers a generic and intuitive solution for cross-platform omics data analysis. It has functions for import, preprocessing, exploration, contrast analysis and visualization of omics data. It follows a tidy, functional programming paradigm.

Author: Aditya Bhagwat [aut, cre], Shahina Hayat [aut], Anna Halama [ctb], Richard Cotton [ctb], Laure Cougnaud [ctb], Rudolf Engelke [ctb], Hinrich Goehlmann [sad], Karsten Suhre [sad], Johannes Graumann [aut, sad, rth]

Maintainer: Aditya Bhagwat <aditya.bhagwat at mpi-bn.mpg.de>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	using_autonomics
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, DimensionReduction, GeneExpression, MassSpectrometry, Preprocessing, PrincipalComponent, RNASeq, Software, Transcription
Version	1.0.1
In Bioconductor since	BioC 3.13 (R-4.1) (< 6 months)
License	GPL-3
Depends	R (>= 4.0)
Imports	abind, assertive, BiocFileCache, BiocGenerics, colorspace, data.table, edgeR, ggplot2, ggrepel, graphics, grDevices, grid, gridExtra, limma, magrittr, matrixStats, methods, MultiAssayExperiment, parallel, pcaMethods, rappdirs, rlang, R.utils, readxl, S4Vectors, scales, stats, stringi, SummarizedExperiment, tidyr, tools, utils
LinkingTo
Suggests	affy, AnnotationDbi, BiocManager, diagram, GenomicRanges, GEOquery, hgu95av2.db, ICSNP, knitr, lme4, lmerTest, MASS, mixOmics, mpm, nlme, org.Hs.eg.db, org.Mm.eg.db, RCurl, remotes, rmarkdown, ropls, Rsubread, rtracklayer, seqinr, statmod, testthat
SystemRequirements
Enhances
URL	https://github.com/bhagwataditya/autonomics
BugReports	https://bitbucket.org/graumannlabtools/autonomics
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	autonomics_1.0.1.tar.gz
Windows Binary
macOS 10.13 (High Sierra)	autonomics_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/autonomics
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/autonomics
Package Short Url	https://bioconductor.org/packages/autonomics/
Package Downloads Report	Download Stats