genomicInstability

DOI: 10.18129/B9.bioc.genomicInstability    

Genomic Instability estimation for scRNA-Seq

Bioconductor version: Release (3.14)

This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.

Author: Mariano Alvarez [aut, cre], Pasquale Laise [aut], DarwinHealth [cph]

Maintainer: Mariano Alvarez <reef103 at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("genomicInstability")

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("genomicInstability")

 

PDF R Script Using genomicInstability
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews GeneExpression, SingleCell, Software, SystemsBiology
Version 1.0.0
In Bioconductor since BioC 3.14 (R-4.1) (< 6 months)
License file LICENSE
Depends R (>= 4.1.0), checkmate
Imports mixtools, SummarizedExperiment
LinkingTo
Suggests SingleCellExperiment, ExperimentHub, pROC
SystemRequirements
Enhances
URL https://github.com/DarwinHealth/genomicInstability
BugReports https://github.com/DarwinHealth/genomicInstability
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 genomicInstability_1.0.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra) genomicInstability_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/genomicInstability
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/genomicInstability
Package Short Url https://bioconductor.org/packages/genomicInstability/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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