genomicInstability-package: genomicInstability: Genomic Instability estimation for...

In reef103/genomicInstability: Genomic Instability estimation for scRNA-Seq

genomicInstability: Genomic Instability estimation for scRNA-Seq

Description

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.

Details

The basic functionality of this package can be performed by inferCNV(), to infer the enrichment of loci-blocks on gene expresion; genomicInstabilityScore(), to estimate the genomic instability for each of the cells in the scRNASeq dataset; giLikelihood(), to estimate the relative likelihood for each cell to be normal (low genomic instability) or tumor (high genomic instability); plot() and giDensityPlot() to plot the scores per loci-block and the distribution of the genomic instability score, respectively.

Author(s)

Maintainer: Mariano Alvarez [e-mail]

Authors:

• Pasquale Laise [e-mail]

Other contributors:

• DarwinHealth [copyright holder]

See Also

[inferCNV()] for estimating loci-block enrichment, [genomicInstabilityScore()] for estimating the genomic instability of each cell in the dataset, [giLikelihood()] for estimating the relative likelihood for the cells to be normal or neoplastic, [plot.inferCNV()] and [giDensityPlot()] to plot the results.

reef103/genomicInstability documentation built on Oct. 10, 2022, 12:33 a.m.