genomicInstability

Genomic Instability estimation for scRNA-Seq

Bioconductor version: Release (3.17)

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 "4.3") and enter:

if (!require("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")

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

Details

biocViews	GeneExpression, SingleCell, Software, SystemsBiology
Version	1.6.0
In Bioconductor since	BioC 3.14 (R-4.1) (2 years)
License	file LICENSE
Depends	R (>= 4.1.0), checkmate
Imports	mixtools, SummarizedExperiment
Linking To
Suggests	SingleCellExperiment, ExperimentHub, pROC
System Requirements
Enhances
URL	https://github.com/DarwinHealth/genomicInstability
Bug Reports	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_1.6.0.tar.gz
Windows Binary	genomicInstability_1.6.0.zip
macOS Binary (x86_64)	genomicInstability_1.6.0.tgz
macOS Binary (arm64)	genomicInstability_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/genomicInstability
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/genomicInstability
Bioc Package Browser	https://code.bioconductor.org/browse/genomicInstability/
Package Short Url	https://bioconductor.org/packages/genomicInstability/
Package Downloads Report	Download Stats