Software Packages

• 

  BOUQUET

  Building Optimized Units of Quantified Enhancer Topologies

  GitHub
  PrePrint
  • Builds cis-regulatory element communities for each expressed gene using loop-derived connections
  • Ranks communities by ChIP-Seq/CUT&RUN signal
  • Identifies 3D-Super-Enhancers
• 

  SEASEQ / PEASEQ

  Single-End Antibody SEQuencing analysis pipeline
  Paired-End Antibody SEQuencing analysis pipeline
  

  GitHub
  Manuscript
  • Basic analysis of ChIP-Seq or CUT&RUN data
  • Alignment with bowtie
  • Coverage tracks including reads-per-million normalization
  • Peak calling with MACS
  • Island-calling with SICER2
  • Motif enrichment with MEME
  • Super-enhancer-like region-detection with ROSE2
• 

  ROSE

  Rank Ordering of Super-Enhancers

  GitHub
  
  • Fork of original SE code
  • Refer to original citations for background
  • Upgraded to python3
  • Dockerized
• 

  HiLOW

  HiC/HiChIP Looping Organization Workflow

  GitHub
  PrePrint
  • Basic analysis of HiC/HiChIP data from FASTQ to .hic contact map
  • High-confidence loop calls for HiChIP using flexible anchor identification
• 

  LASER

  Loci ATAC-Seq Enrichment Resampling

  GitHub
  PrePrint
  • Log odds ratio calculator for pair-wise co-accessibility analysis in single-cell ATAC-Seq data