RMT package: extract combinatorial RNA methylome from multiple MeRIP-Seq datasets RMT is now part of exomePeak package. Install the current exomePeak package from Bioconductor to ensure all the dependencies are properly installed
source("http://bioconductor.org/biocLite.R")
biocLite("GenomicAlignments")
biocLite("exomePeak")
Install devtools
install.packages("devtools")
Install the developmental version of exomePeak
library(devtools)
install_github('lzcyzm/exomePeak')
the package should be ready to go now
library(exomePeak)
?RMT # please check the description of RMT
example(RMT) # an example
Alternatively, exomePeak package can automatically download the complete transcriptome. And then scan the entire transcriptome for RNA methylation sites. It will take a long time
RMT(INPUT_BAM=input_bam, IP_BAM=ip_bam, INPUT2IP=input2bam, GENOME="hg19")