BIMSBbioinfo/reg2gene: Predicting the target genes for regulatory elements

reg2gene R package was build to perform 2 main categories of tasks: - 1. to predict target genes for regulatory elements genome-wide by building "gene expression - enhancer activity" models by performing: - DATA INTEGRATION - extracting information stored in bigWig files (across different cell types) to - a. quantifying (enhancer) activity (regulatory potential) for genomic regions of interest (enhancer regions), and - b. quantifying gene expression for genes of interest, and/or - c. combining these informations into one object used further for modelling - DATA MODELLING (including performance assessment) - modelling gene expression - enhancer activity using different algorithms, and combine different models with meta-analysis and voting procedure. Additionally, one can benchmark results and obtain confusion matrix. - DATA VISUALIZATION - visualization of interactions as loops in the context of the genome - 2. to annotate genomic regions (ChIP-Seq peaks or similar regions in the genome) to genes they are associated with based on the modelled enhancer-gene associations. Optionally one can as well associate genes with diseases reported in the disease-gene databases.

Getting started

Package details

Authorperson("Inga", "Patarcic", email = "[email protected]", role = c("aut", "cre"), person("Altuna", "Akalin", email = "[email protected]", role=c("aut", "cre"))))
MaintainerInga Patarcic <[email protected]>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
BIMSBbioinfo/reg2gene documentation built on May 10, 2018, 8:02 a.m.