chromVAR
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GreenleafLab
chromatin Variability Across Regions (of the genome!)
I've been having problems installing chromVAR. Below is the output that I'm getting. Any idea on how I can install it???? BiocInstaller::biocLite("GreenleafLab/chromVAR") BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.1), R...
"In order to be able to use the filterSamples function, a “depth” column with the total sequencing depth must be included in the colData in the SummarizedExperiment object." I already...
I'm trying to use ChromVAR to read in output from the 10X cellranger-atac pipeline. I believe I have it working when reading in the peak_bc_matrix as my own count table,...
I have filtered my bulk ATAC-seq bam files by removing the duplicates and all reads in chrM. But my bam files don't have a @RG header information. So I didn't...
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:...
What step in the pipeline is the ATAC-seq counts normalized? And what is the method used? If I needed a normalized count list, can I just pull from the counts...
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...
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chromatin Variability Across Regions (of the genome!)