TOBIAS 0.13.3-foss-2021b

TOBIAS is a collection of command-line bioinformatics tools for performing footprinting analysis on ATAC-seq data, and includes: Correction of Tn5 insertion bias; Calculation of footprint scores within regulatory regions; Estimation of bound/unbound transcription factor binding sites; and Visualization of footprints within and across different conditions

Accessing TOBIAS 0.13.3-foss-2021b

To load the module for TOBIAS 0.13.3-foss-2021b please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load TOBIAS/0.13.3-foss-2021b

BEAR Apps Version

2021a

Extensions

  • configs 3.0.3
  • kneed 0.7.0
  • logomaker 0.8
  • MOODS-python-1.9.4.1
  • PyPDF2 1.26.0
  • reportlab 3.6.2
  • statistics 1.0.3.5
  • svist4get 1.2.24
  • TOBIAS 0.13.3
  • Wand 0.6.7

More Information

For more information visit the TOBIAS website.

Dependencies

This version of TOBIAS has a direct dependency on: adjustText/0.7.3-foss-2021b Biopython/1.79-foss-2021b boto3/1.20.13-GCCcore-11.2.0 foss/2021b ImageMagick/7.1.0-4-GCCcore-11.2.0 pybedtools/0.8.2-GCC-11.2.0 pyBigWig/0.3.18-foss-2021b Pysam/0.17.0-GCC-11.2.0 Python/3.9.6-GCCcore-11.2.0 PyYAML/5.4.1-GCCcore-11.2.0 scikit-learn/1.0.1-foss-2021b SciPy-bundle/2021.10-foss-2021b Seaborn/0.11.2-foss-2021b XlsxWriter/3.0.2-GCCcore-11.2.0

Last modified on 23rd August 2022