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>
citation("OMICsPCA")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| OMICsPCA | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
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) (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 |
| System Requirements | |
| URL |
See More
| Suggests | knitr, RUnit, BiocGenerics |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/OMICsPCA/ |
| Package Short Url | https://bioconductor.org/packages/OMICsPCA/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |