README.md

In lixin4306ren/seqana:

seqana

chip-seq, bs-seq, rna-seq processing scripts

installation

library("devtools")
install_github("lixin4306ren/seqana")

chip-seq related functions

1. diff_peaks_replicate merge peaks based on replicates and find differentially peaks between 2 samples
2. merge_peaks merge neighbouring peaks to large one by given distance
3. get_common_peak3 extract common peaks based on replicates
4. cal.rpkm.chip this function calculate RPKM for chip-seq data, support bam and bed input format
5. annotatePeaks find nearest gene asscosiated with given peaks, deault database is human.gencodeV19

bs-seq related functions

1. plot_meth_sliding_bsseq plot and calculate methylation along sliding windows from bsseq object
2. meth_count_region_for_bsseq calculate methylation level based on given Grange from bsseq object

rna-seq related funtions

utility functions

1. generate.sliding.window generate sliding window ranges
2. bedtools.coveragebed.range calculate overlap % between 2 bed files, need bedtools installed
3. bedtools.coveragebed calculate overlap % between 2 bed files, need bedtools instal

lixin4306ren/seqana documentation built on May 20, 2019, 3:32 p.m.