ChIP-seq

ChIP-exo data analysis

Our neighboring lab just generated some ChIP-exo data, (if you do not know the technique, look at this paper ) and the company did some analysis but not…

compare ChIP-seq data for different conditions and different transcription factors?

I have done a lot of ChIP-seq data analysis, but most of them are just mapping to reference genome and then calling peaks (use MACS from Shirley liu’s lab…

finding the closest feature given a set of Genomic coordinates

I have a bed file which contains peak information for a ChIP-seq data. I want to find the genes that are closest to these peaks.

reproduce k-means clustering and heatmap

I asked this question in seqanswer and biostar

A new peak calling software: peakzilla

How to make a heatmap based on ChIP-seq data by R

update on 04/20/2016.\ I noticed that this post is the most frequently visited one. it has been almost 3 years\ since I wrote this post. Now, there are…

jMOSAiCS: joint analysis of multiple ChIP-seq datasets

it is a R package, may consider to use it.

make an average conservation plot based on ChIP-seq data

I asked this question at Seqanswer

Statistical measure of biological significance for overlapping genomic regions

updated 06/25/13 look at this python package, it answered this question

How to make TSS plot using RNA-seq and ChIP-seq data

many times, we want to plot the ChIP-seq signal across the TSS in a genome wide scale.