Comparing Many Bed Files from GEO
Hello, I am interested in comparing many ATAC-seq bed files on GEO to see which peaks are present across many studies. The best way so far I have found is to use CHIPseeker's "Data Mining with ChIP seq data deposited in GEO" capability as described in the CHIPseeker Vignette Does anyone have any experience with this part of chipseeker or have you tried meta-analysis of BED files before? If so, which package/program did you use? And were there any tutorials you found helpful?
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