OMICsPCA

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

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

Bioconductor version: Development (3.18)

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>

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

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("OMICsPCA")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Details

biocViews	BiologicalQuestion, BiomedicalInformatics, Clustering, DataRepresentation, DimensionReduction, Epigenetics, EpigeneticsWorkflow, FunctionalGenomics, GUI, GeneticVariability, ImmunoOncology, MultipleComparison, PrincipalComponent, SingleCell, Software, Transcription, Visualization, Workflow
Version	1.19.0
In Bioconductor since	BioC 3.8 (R-3.5) (5 years)
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
Linking To
Suggests	knitr, RUnit, BiocGenerics
System Requirements
Enhances
URL

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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary	OMICsPCA_1.19.0.zip (64-bit only)
macOS Binary (x86_64)	OMICsPCA_1.19.0.tgz
macOS Binary (arm64)	OMICsPCA_1.19.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/OMICsPCA
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OMICsPCA
Bioc Package Browser	https://code.bioconductor.org/browse/OMICsPCA/
Package Short Url	https://bioconductor.org/packages/OMICsPCA/
Package Downloads Report	Download Stats