ASPEN development version

ASPEN 1.0.6

  • fix: dockername typo (#57, @kopardev)
  • docs: update documentation, change theme (#77, #78, @kopardev)

ASPEN 1.0.5

  • fix: ucsc tool version changed requiring newer version of GLIBC (#54, @kopardev)
  • using new masterdocker v11

ASPEN 1.0.4

  • fix: DiffATAC failure (#46, @kopardev)
  • fix: last line of contrasts.tsv read in correctly; black lines ignored (#48, @kopardev)
  • fix: ROI calculation from fixed-width consensus peaks no longer tried to fix the peak width again (#50, @kopardev)
  • feature: create diffatac results from MACS2 peaks (#51, @kopardev)
  • fix: BUYINPARTITIONS fixed in wrapper for BIOWULF-only (#52, @kopardev)

ASPEN 1.0.3

  • fix: No module named 'numpy._core._multiarray_umath' error withunset PYTHONPATH (#43, @kopardev)
  • fix: jobby command points to the correct location of snakemake.log file
  • ASPEN is now archived on Zenodo, you can cite it with the DOI 10.5281/zenodo.13755867. (#42, @kelly-sovacool)

ASPEN 1.0.2

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)