autonomics

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see autonomics.

Generifying and intuifying cross-platform omics analysis

Bioconductor version: 3.14

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 (!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")

using_autonomics HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DimensionReduction, GeneExpression, MassSpectrometry, Preprocessing, PrincipalComponent, RNASeq, Software, Transcription

Version 1.2.0

In Bioconductor since BioC 3.13 (R-4.1) (3 years)

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

System Requirements

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

Bug Reports https://bitbucket.org/graumannlabtools/autonomics

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

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_1.2.0.tar.gz

Windows Binary autonomics_1.2.0.zip

macOS 10.13 (High Sierra) autonomics_1.2.0.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

Old Source Packages for BioC 3.14 Source Archive