autonomics

DOI: 10.18129/B9.bioc.autonomics    

This is the development version of autonomics; to use it, please install the devel version of Bioconductor.

Generifying and intuifying cross-platform omics analysis

Bioconductor version: Development (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>

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

Installation

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

if (!requireNamespace("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")

 

HTML R Script using_autonomics
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DimensionReduction, GeneExpression, MassSpectrometry, Preprocessing, PrincipalComponent, RNASeq, Software, Transcription
Version 0.99.22
In Bioconductor since BioC 3.13 (R-4.1)
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_0.99.22.tar.gz
Windows Binary
macOS 10.13 (High Sierra) autonomics_0.99.22.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: