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autonomics

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

Generifying and intuifying cross-platform omics analysis

Bioconductor version: Development (3.18)

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 uni-marburg.de>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
using_autonomics HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, DimensionReduction, GeneExpression, MassSpectrometry, Preprocessing, PrincipalComponent, RNASeq, Software, Transcription
Version 1.9.0
In Bioconductor since BioC 3.13 (R-4.1) (2 years)
License GPL-3
Depends R (>= 4.0)
Imports abind, assertive, BiocFileCache, BiocGenerics, bit64, colorspace, data.table, dplyr, 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
Linking To
Suggests affy, AnnotationDbi, BiocManager, BiocStyle, 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
System Requirements
Enhances
URL https://github.com/bhagwataditya/autonomics
Bug Reports https://bitbucket.org/graumannlabtools/autonomics
See More
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_1.9.0.tar.gz
Windows Binary autonomics_1.9.0.zip
macOS Binary (x86_64) autonomics_1.9.0.tgz
macOS Binary (arm64) autonomics_1.9.0.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