chip-seq, bs-seq, rna-seq processing scripts
library("devtools")
install_github("lixin4306ren/seqana")
diff_peaks_replicate
merge peaks based on replicates and find differentially peaks between 2 samplesmerge_peaks
merge neighbouring peaks to large one by given distanceget_common_peak3
extract common peaks based on replicatescal.rpkm.chip
this function calculate RPKM for chip-seq data, support bam and bed input formatannotatePeaks
find nearest gene asscosiated with given peaks, deault database is human.gencodeV19plot_meth_sliding_bsseq
plot and calculate methylation along sliding windows from bsseq objectmeth_count_region_for_bsseq
calculate methylation level based on given Grange from bsseq objectgenerate.sliding.window
generate sliding window rangesbedtools.coveragebed.range
calculate overlap % between 2 bed files, need bedtools installedbedtools.coveragebed
calculate overlap % between 2 bed files, need bedtools instalAdd the following code to your website.
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