Welcome to the new bioconductor.org!

genomicInstability

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

Genomic Instability estimation for scRNA-Seq


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
See More
Suggests SingleCellExperiment, ExperimentHub, pROC
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 genomicInstability_1.9.0.tar.gz
Windows Binary genomicInstability_1.9.0.zip (64-bit only)
macOS Binary (x86_64) genomicInstability_1.9.0.tgz
macOS Binary (arm64)
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