CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

This package provides gene set analysis, enriched subnetwork analyses and 'Time-series' functional analysis for various preprocessed high-throughput data generated either by CRISPR screening, RNA-seq, micro-array or RNAi in a unified workflow. 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 <>, Feng GAO <>, Xiupei MEI <>, Xin Wang <>
Bioconductor views CRISPR GO GeneExpression GeneSetEnrichment KEGG NetworkEnrichment TimeCourse
MaintainerLina ZHU <>
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. 3, 2020, 2:35 a.m.