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intePareto (version 0.0.1)

Integrative Analysis of RNA-Seq and ChIP-Seq Data

Description

Integrative analysis of gene expression (RNA-Seq data), and histone modification data for user-defined sets of histone marks (ChIP-Seq data) to discover consistent changes in genes between biological conditions. Additionally, Pareto optimization is used to prioritize genes based on the level of consistent changes in both RNA-Seq and ChIP-Seq data.

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Version

Install

install.packages('intePareto')

Monthly Downloads

27

Version

0.0.1

License

GPL (>= 2)

Maintainer

Yingying Cao

Last Published

October 9th, 2019

Functions in intePareto (0.0.1)

df_final

an example of the result of doIntegration
test_rna_meta

meta data of preprocessed RNA-Seq data
promoter

an example of promoter region
res

an example of the result of doMatch
counts2lFC

Calculate log2FoldChange
bam2rpm

Compute the normalized number of reads (rpm) fall into specific genomic region
doIntegration

Do integrative analysis
test_chip_meta

meta data of preprocessed ChIP-Seq data
bam2counts

Compute the number of reads fall into specific genomic region
doPareto

Prioritization of genes based on Z scores
doMatch

Match the RNA-Seq and ChIP-Seq data on the gene level