genomicInstability
Genomic Instability estimation for scRNA-Seq
Bioconductor version: Release (3.20)
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("genomicInstability")):
Installation
To install this package, start R (version "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, SingleCell, Software, SystemsBiology |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (3 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_1.12.0.tar.gz |
| Windows Binary (x86_64) | genomicInstability_1.12.0.zip |
| macOS Binary (x86_64) | genomicInstability_1.12.0.tgz |
| macOS Binary (arm64) | genomicInstability_1.12.0.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 |