Are there pipelines to analyze the Quality Controls for ATAC-seq and ChIP-seq data?

Question

[Dan]

Hello:

Are there pipelines to analyze all of the Quality Controls for ATAC-seq and ChIP-seq data in cistrome db? http://cistrome.org/db/#/ I know fastqc to analyze the sequence quality, qualimap bamqc to analysis the mapping quality, are there some pipelines or tools (R, python, or bash) to analyze the number of peaks with good enrichment, fraction of reads in peaks and DNase-seq hypersensitive sites overlapped ratio in peaks? Is ChiLin(https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1274-4) still the best choice?

Thanks a lot

[Papyrus]

In R, I know of ChIPQC to generate reports with good plots and statistical summaries of ChIP-seq QC variables.