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

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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.

Author
Lin Zhang <lin.zhang@cumt.edu.cn>, Lian Liu <liulian19860905@163.com>, Jia Meng <jia.meng@xjtlu.edu.cn>
Date of publication
None
Maintainer
Lin Zhang <lin.zhang@cumt.edu.cn>, Lian Liu <liulian19860905@163.com>, Jia Meng <jia.meng@xjtlu.edu.cn>
License
GPL-2
Version
2.8.0

View on Bioconductor

Man pages

bltest
bltest
ctest
ctest
exomepeak
exomepeak
exomePeak-package
exomePeak
rhtest
rhtest
RMT
Extract a combinatorial RNA methylome from multiple...

Files in this package

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