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autonomics
This is thereleased version of autonomics; for the devel version, seeautonomics.
Unified Statistical Modeling of Omics Data
Bioconductor version: Release (3.22)
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). Across clustering methods (hclust, pam, cmeans). Across survival methods (coxph, survdiff, coin). It provides a fast enrichment analysis implementation.
Author: Aditya Bhagwat [aut, cre], Richard Cotton [aut], Vanessa Beutgen [ctb], Witold Szymanski [ctb], Shahina Hayat [ctb], Laure Cougnaud [ctb], Hinrich Goehlmann [sad], Karsten Suhre [sad], Johannes Graumann [aut, sad]
Maintainer: Aditya Bhagwat <aditya.bhagwat at uni-marburg.de>
citation("autonomics")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("autonomics")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport,DifferentialExpression,DimensionReduction,GeneExpression,GeneSetEnrichment,MassSpectrometry,Metabolomics,Microarray,Preprocessing,PrincipalComponent,Proteomics,RNASeq,Regression,Software,Transcription,Transcriptomics |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (4.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | abind,arrow,BiocFileCache,BiocGenerics,bit64,cluster,codingMatrices,colorspace,data.table,dplyr,edgeR,ggforce,ggplot2,ggrepel, graphics, grDevices, grid,gridExtra,limma,lme4,magrittr,matrixStats, methods,MultiAssayExperiment, parallel,RColorBrewer,rlang,R.utils,readxl,S4Vectors,scales, stats,stringi,SummarizedExperiment,survival,tidyr,tidyselect, tools, utils,vsn |
| System Requirements | |
| URL | |
| Bug Reports | https://gitlab.uni-marburg.de/fb20/ag-graumann/software/autonomics/issues |
See More
| Suggests | affy,AnnotationDbi,AnnotationHub,apcluster,Biobase,BiocManager,BiocStyle,Biostrings,coin,diagram,DBI,e1071,ensembldb,GenomicDataCommons,GenomicRanges,GEOquery,ggstance,ggridges,ggtext,hgu95av2.db,ICSNP,jsonlite,knitr,lmerTest,MASS,mclust,mixOmics,mixtools,mpm,nlme,OlinkAnalyze,org.Hs.eg.db,org.Mm.eg.db,patchwork,pcaMethods,pheatmap,progeny,propagate,RCurl,RSQLite,remotes,rmarkdown,ropls,Rsubread,readODS,rtracklayer,statmod,testthat,UniProt.ws,writexl,XML |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | autonomics_1.18.0.tar.gz |
| Windows Binary (x86_64) | autonomics_1.18.0.zip |
| macOS Binary (x86_64) | autonomics_1.18.0.tgz |
| macOS Binary (arm64) | autonomics_1.18.0.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 |