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OpenOmics / chrom-seek

An awesome set of epigenetic pipelines for bulk cfChip-seq, ChIP-seq, and ATAC-seq
https://openomics.github.io/chrom-seek/
MIT License
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Additional functionality for cfChIP #33

Closed tovahmarkowitz closed 1 month ago

tovahmarkowitz commented 7 months ago

The new features to be added to the cfChIP assay include:

  1. Run a DiffBind R script on all "ChIP" samples to:
    • Identify consensus peaks, produce bed file
    • Get normalized counts per sample
    • Get UMAP coordinates based upon this information
  2. Annotate consensus peaks with uropa
  3. Run Amos's specialized differential RMD
  4. If only one group per sample and all samples have a group, create UMAP plot