CityUHK-CompBio/HTSanalyzeR2: An R package for gene set enrichment and network analysis of various high-throughput data

This package provides classes and methods for gene set over-representation, enrichment and network analyses on various high-throughput data as well as corresponding time-series data generated by CRISPR, RNAi, RNA-seq and micro-array. The over-representation analysis is based on hypergeometric test and the enrichment analysis is based on the GSEA algorithm published by (Subramanian et al.PNAS 2005). The network analysis could identify the enriched subnetworks based on the algorithms from BioNet package(Beisser et al., Bioinformatics 2010). A pipeline function is provided for CRISPR data preprocessed by MAGeCK, which is seamless linked with MAGeCK. Time series data analysis could also be performed for better mutual comparison. Finally, a dynamic shiny report could be generated encompassing all the results, allowing users to modify the visualization part and download results in different formats.

Getting started

Package details

AuthorLina ZHU <[email protected]>, Feng GAO <[email protected]>, Xiupei MEI <[email protected]>, Xin Wang <[email protected]>
Bioconductor views CRISPR GO GeneExpression GeneSetEnrichment KEGG NetworkEnrichment TimeCourse
MaintainerLina ZHU <[email protected]>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 11, 2018, 8:06 a.m.