Exome-based Analysis for RNA Epigenome Sequencing Data
ExomePeak was originally a MATLAB toolbox distributed under the free GNU GPL license for affinity-based RNA epigenome sequencing data obtained from MeRIP-seq  or m6A-seq  . It is now also available as an R-package to achieve the complete open source capacity. The MATLAB-based exomePeak package  is no longer actively maintained.
The salient features of exomePeak R-package include:
ExomePeak detects a single peak that spans 2 junctions, compared with the genome-based method MACS2 that reports 3 non-adjacent peaks, all of which cover some intronic regions.
The exomePeak R-package is now available from bioconductor and can be installed with the following R commands:
The usage of exomePeak package is very straightforward. It takes directly the ouput of spliced aligner such as Tophat, and outputs exome-based peaks or binding sites in BED format.
# For peak detection:
where, gtf, ip and input are the gene annotation GTF file, IP bam files and input control bam files, respectively.
# for peak calling and comparing two experimental conditions
# where, gtf, ip and input are the gene annotation GTF file, IP bam files and input control bam files, respectively. And treated_ip and treated_input are the IP and control bam files from a differential condition.
User support is available from Google group: "RNA epigenetics and Post-transcriptional RNA modifications"
The exome R-package is under active development, we welcome any suggestions or questions. Please feel free to contact Dr. Jia Meng (Email: email@example.com) for any questions.
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2. Dominissini, Dan; Moshitch-Moshkovitz, Sharon; Schwartz, Schraga; Salmon-Divon, Mali; Ungar, Lior; Osenberg, Sivan; Cesarkas, Karen; Jacob-Hirsch, Jasmine; Amariglio, Ninette; Kupiec, Martin; Sorek, Rotem; Rechavi, Gideon (28 April 2012). "Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq". Nature 485 (7397): 201 206. doi:10.1038/nature11112.