Skip to content

compgenomics/MeTPeak

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code
This branch is 9 commits ahead, 4 commits behind arlston:master.

Latest commit

 

Git stats

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
R
 
 
 
 
 
 
man
 
 
 
 
 
 
 
 

MeTPeak

Version: 1.1

Date: 2016-2-2

Author: Xiaodong Cui xiaodong.cui@outlook.com, Jia Meng jia.meng@hotmail.com

Maintainer: Xiaodong Cui xiaodong.cui@outlook.com

The package is developed for the finding the location of m6A sites in MeRIP-seq data

License: GPL-2

Depends: Rsamtools, GenomicFeatures (>= 1.0.0), rtracklayer, BH, RcppArmadillo, Rcpp

Installation

R package devtools is required for metpeak to be installed from GitHub.

install.packages("devtools")

Some of MeTPeak dependent packages have to be installed from BiocLite, At last, MeTPeak can be installed as:

library("devtools")
source("https://bioconductor.org/biocLite.R")
install_github("compgenomics/MeTPeak",build_opts = c("--no-resave-data", "--no-manual"))

Toy Example

# using the data included in the package
library(MeTPeak)

# in the real case, change the gtf to what you need
gtf <- system.file('extdata','example.gtf',package='MeTPeak')

ip1 <- system.file('extdata','IP1.bam',package='MeTPeak')
ip2 <- system.file('extdata','IP2.bam',package='MeTPeak')
ip3 <- system.file('extdata','IP3.bam',package='MeTPeak')
input1 <- system.file('extdata','Input1.bam',package='MeTPeak')
input2 <- system.file('extdata','Input2.bam',package='MeTPeak')
input3 <- system.file('extdata','Input3.bam',package='MeTPeak')

IP_BAM <- c(ip1,ip2,ip3)
INPUT_BAM <- c(input1,input2,input3)

metpeak(GENE_ANNO_GTF=gtf,IP_BAM = IP_BAM,INPUT_BAM = INPUT_BAM,
        EXPERIMENT_NAME="example")

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages

  • R 100.0%