OMICsPCA

DOI: 10.18129/B9.bioc.OMICsPCA    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see OMICsPCA.

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

Bioconductor version: 3.9

OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it's core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals.

Author: Subhadeep Das [aut, cre], Dr. Sucheta Tripathy [ctb]

Maintainer: Subhadeep Das <subhadeep1024 at gmail.com>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("OMICsPCA")

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("OMICsPCA")

 

HTML	R Script	OMICsPCA
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiologicalQuestion, BiomedicalInformatics, Clustering, DataRepresentation, DimensionReduction, Epigenetics, EpigeneticsWorkflow, FunctionalGenomics, GUI, GeneticVariability, ImmunoOncology, MultipleComparison, PrincipalComponent, SingleCell, Software, Transcription, Visualization, Workflow
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
License	GPL-3
Depends	R (>= 3.5.0), OMICsPCAdata
Imports	HelloRanges, fpc, stats, MultiAssayExperiment, pdftools, methods, grDevices, utils, clValid, NbClust, cowplot, rmarkdown, kableExtra, rtracklayer, IRanges, GenomeInfoDb, reshape2, ggplot2, factoextra, rgl, corrplot, MASS, graphics, FactoMineR, PerformanceAnalytics, tidyr, data.table, cluster, magick
LinkingTo
Suggests	knitr, RUnit, BiocGenerics
SystemRequirements
Enhances
URL
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	OMICsPCA_1.2.0.tar.gz
Windows Binary	OMICsPCA_1.2.0.zip
Mac OS X 10.11 (El Capitan)	OMICsPCA_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OMICsPCA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OMICsPCA
Package Short Url	https://bioconductor.org/packages/OMICsPCA/
Package Downloads Report	Download Stats