exomePeak: exome-based anlaysis of MeRIP-Seq data: peak calling and differential analysis

The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng <jia.meng@hotmail.com> if you have any questions.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("exomePeak")
AuthorLin Zhang <lin.zhang@cumt.edu.cn>, Lian Liu <liulian19860905@163.com>, Jia Meng <jia.meng@xjtlu.edu.cn>
Bioconductor views HighThroughputSequencing Methylseq RNAseq Sequencing
Date of publicationNone
MaintainerLin Zhang <lin.zhang@cumt.edu.cn>, Lian Liu <liulian19860905@163.com>, Jia Meng <jia.meng@xjtlu.edu.cn>
LicenseGPL-2
Version2.10.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/RMT.R R/bed2transcriptdb.R R/bltest.r R/ctest.R R/diff.consistency.evaluate.R R/divide.anno.into.batches.R R/exomepeak.R R/exomepeak_notification.R R/get.bam.chrs.R R/get.bam.read.length.R R/get.block.from.rna.peak.R R/get.check.points.R R/get.check.points.reads.count.R R/get.gene.anno.R R/get.peak.from.loci.R R/get.peak.reads.count.R R/get.reads.count.R R/get.sample.id.R R/get.table.peak.result.R R/merge.and.compare.two.different.conditions.R R/peak.calling.module.R R/read.gtf.R R/remove.local.anomalities.R R/report.diff.peak.based.on.result.R R/report.peak.based.on.result.R R/rhtest.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/exomePeak-Overview.R
inst/doc/exomePeak-Overview.Rnw
inst/doc/exomePeak-Overview.pdf
inst/extdata
inst/extdata/IP1.bam
inst/extdata/IP1.bam.bai
inst/extdata/IP2.bam
inst/extdata/IP2.bam.bai
inst/extdata/IP3.bam
inst/extdata/IP3.bam.bai
inst/extdata/IP4.bam
inst/extdata/IP4.bam.bai
inst/extdata/Input1.bam
inst/extdata/Input1.bam.bai
inst/extdata/Input2.bam
inst/extdata/Input2.bam.bai
inst/extdata/Input3.bam
inst/extdata/Input3.bam.bai
inst/extdata/example.gtf
inst/extdata/treated_IP1.bam
inst/extdata/treated_IP1.bam.bai
inst/extdata/treated_Input1.bam
inst/extdata/treated_Input1.bam.bai
man
man/RMT.Rd man/bltest.Rd man/ctest.Rd man/exomePeak-package.Rd man/exomepeak.Rd man/rhtest.Rd
vignettes
vignettes/exomePeak-Overview.Rnw
vignettes/exomePeak_output
vignettes/exomePeak_output/con_peak.bed
vignettes/exomePeak_output/con_peak.xls
vignettes/exomePeak_output/con_sig_diff_peak.bed
vignettes/exomePeak_output/con_sig_diff_peak.xls
vignettes/exomePeak_output/diff_peak.bed
vignettes/exomePeak_output/diff_peak.xls
vignettes/exomePeak_output/exomePeak.Rdata
vignettes/exomePeak_output/peak.bed
vignettes/exomePeak_output/peak.xls
vignettes/exomePeak_output/sig_diff_peak.bed
vignettes/exomePeak_output/sig_diff_peak.xls

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.