genomicInstability

This is the released version of genomicInstability; for the devel version, see genomicInstability.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14

Genomic Instability estimation for scRNA-Seq

Bioconductor version: Release (3.23)

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")):

Mariano Alvarez, Pasquale Laise. genomicInstability: Genomic Instability estimation for scRNA-Seq. doi:10.18129/B9.bioc.genomicInstability, R package version 1.18.0, https://bioconductor.org/packages/genomicInstability.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, SingleCell, Software, SystemsBiology
Version	1.18.0
In Bioconductor since	BioC 3.14 (R-4.1) (5 years)
License	file LICENSE
Depends	R (>= 4.1.0), checkmate
Imports	mixtools, SummarizedExperiment
System Requirements
URL	https://github.com/DarwinHealth/genomicInstability
Bug Reports	https://github.com/DarwinHealth/genomicInstability

Suggests	SingleCellExperiment, ExperimentHub, pROC
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	genomicInstability_1.18.0.tar.gz
Windows Binary (x86_64)	genomicInstability_1.18.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	genomicInstability_1.18.0.tgz
macOS Binary (sonoma-arm64)	genomicInstability_1.18.0.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