PEGS: Peak-set Enrichment of Gene-Sets

PEGS (Peak-set Enrichment of Gene-Sets) is a Python bioinformatics utility for calculating enrichments of gene cluster enrichments from peak data at different genomic distances.

• What is PEGS?
  • What it does
  • Citing PEGS
• Getting started
  • Installing PEGS from PyPI using virtualenv and pip
  • Installing PEGS using Conda
  • Installing BEDTOOLS
• Running analyses with PEGS
  • Basic usage
  • Specifying genomic distances (-d, --distances)
  • Specifying TADs (-t, --tads)
  • Specifying output file names (--name, -m, -x)
  • Specifying where output files are written (-o)
• Input files
  • Reference gene intervals file
  • Peak set files
  • Gene cluster files
  • TADs file
• Output files
  • Overview
  • Heatmap
  • XLSX file
  • Optional outputs
• Advanced usage
  • Making gene interval files
  • Customising the heatmap
• Examples
  • Mouse glucocorticoidal dataset
• Known Problems
  • Installation problems
  • Runtime problems
• Version History and Changes
  • Version 0.6.6 (2023-12-07)
  • Version 0.6.5 (2022-07-01)
  • Version 0.6.4 (2021-11-08)
  • Version 0.6.3 (2021-10-25)
  • Version 0.6.2 (2021-09-28)
  • Version 0.6.1 (2021-09-14)
  • Version 0.6.0 (2021-09-14)
  • Version 0.5.1 (2021-05-12)
  • Version 0.5.0 (2021-05-12)
  • Version 0.4.2 (2021-05-12)
  • Version 0.4.1 (2021-05-10)
  • Version 0.4.0 (2020-08-18)
  • Version 0.3.0 (2020-05-13)
  • Version 0.2.0 (2020-03-20)
  • Version 0.1.0 (2020-01-30)