CCR Collaborative Bioinformatics Resource [CCBR]
Published October 15, 2025 | Version v2.7.2
Software Open

CARLISLE: Cut And Run anaLysIS pipeLinE

Creators

  • 1. Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA

Description

  • Fix how singularity bind paths are set. (#187, @kelly-sovacool)
  • Fix the DESeq rule when using the hs1 T2T genome. (#187, @kelly-sovacool, @wong-nw)
  • Fix incorrect jobby version (needs v0.4). (#194, @kelly-sovacool)
  • Fix jobby usage to output stdout/stderr to log file. (#196, @kopardev)
  • Fix numpy error. (#198, @kelly-sovacool)
  • Fix logic error with scaling factor calcutions. (#195, @kopardev)
  • Run MACS2 with control by default. (#195, @kopardev)
  • Make sure submit_slurm.sbatch is not overwritten. (#195, @kopardev)
  • Handle case when sample names are subsets of each other. (#195, @kopardev)

Notes

If you use CARLISLE, please cite it as below.

Files

CCBR/CARLISLE-v2.7.2.zip

Files (124.1 MB)

Name Size Download all
md5:5cf48111da27af55120be6a9eae4e8c7
124.1 MB Preview Download

Additional details

Related works

Is supplement to
Software: https://github.com/CCBR/CARLISLE/tree/v2.7.2 (URL)

Software

Repository URL
https://github.com/CCBR/CARLISLE