intePareto v0.0.1

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Integrative Analysis of RNA-Seq and ChIP-Seq Data

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.

Functions in intePareto

Name Description
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
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Vignettes of intePareto

Name
intePareto.Rmd
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Details

Type Package
Date 2019-10-08
License GPL (>= 2)
LazyLoad yes
NeedsCompilation no
ByteCompile true
Encoding UTF-8
Packaged 2019-10-08 18:20:45 UTC; yingying
RoxygenNote 6.1.1
VignetteBuilder knitr
Repository CRAN
Date/Publication 2019-10-09 16:10:02 UTC

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