Renfang2019

Reading Peaks Files into ChromVAR

1

Dear all, I am trying to read the peak files into ChromVAR, I only get one column on getCounts step. I tried peakfile

DEV at chromVAR

1

> dev

Dear, I am still trying the chromVAR on ATAC data using narrowPeak and bam file. I got the peaks right, please see below. But I could not get the fragment_counts...

Dear, I have been trying the chromVAR for bulk ATAC data and encourter this problem as below. Any suggestions? Thank you so much. library(BSgenome.Mmusculus.UCSC.mm10) > example_counts head((example_counts)) class: RangedSummarizedExperiment dim:...

Dear Alicia, I run the single sample of bulk ATAC and now I would like to run two samples of bulk ATAC data. In your note, you recommend to combine...

ChromVAR data uploading

5

> peaks