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CHANGELOG.md

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ASPEN development version

ASPEN 1.0.2

  • Set the singularity cache dir if --singcache is not provided. (#37, @kelly-sovacool)
  • ASPEN now has a documentation website: https://ccbr.github.io/ASPEN

ASPEN 1.0.1

  • differential ATAC updated
  • documentation updated

ASPEN 1.0.0

  • completely dockerized
  • differential ATAC

ASPEN 0.6.1

  • correction to fqscreen cattle path

ASPEN 0.6

  • support for mmul10 (Macaca) and bosTau9 (cattle) genomes
    • created resource files: indexes, promoter files, tss files etc.
  • Added Macaca and Cattle to fastqscreen indexes
  • support increased from 4 replicate to 6 replicates
  • macs and genrich fixed width peaks generation rule added
  • docker updated to v10 (genome support and tidyverse added)

ASPEN 0.5.3

  • Includes reference files for mmul10

ASPEN 0.5.2

  • atac_assign_multimappers.py now getting query sorted input
  • dryrun log saved in workdir
  • local (workdir) scriptsdir used

ASPEN 0.5.1

  • typo fix in main wrapper script

ASPEN 0.5

  • fastqscreen added
  • minor bug fixes

ASPEN 0.4.1

  • Bug fixes
  • minor updates

ASPEN 0.4

  • Multiqc edits
  • README updates

ASPEN 0.3

  • FRiP calculations added

ASPEN 0.2

  • Peak motif enrichment with homer/meme
  • Peak replicate/sample/peakcaller PCA comparisons after bedtools jaccard pairwise calculations

ASPEN 0.1

  • first working version
  • calls peaks with macs2/genrich
  • annotates peaks with chipseeker (human and mouse support)