leafcutter 0.2.9-foss-2020a-R-4.0.0-Python-2.7.18

Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples.

Accessing leafcutter 0.2.9-foss-2020a-R-4.0.0-Python-2.7.18

To load the module for leafcutter 0.2.9-foss-2020a-R-4.0.0-Python-2.7.18 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load leafcutter/0.2.9-foss-2020a-R-4.0.0-Python-2.7.18

BEAR Apps Version

2020a

Architectures

EL8-cascadelake — EL8-haswell — Ubuntu20.04-haswell

The listed architectures consist of two part: OS-CPU.

  • BlueBEAR: The OS used on BlueBEAR is represented by EL and there are several different processor (CPU) types available on BlueBEAR. More information about the processor types on BlueBEAR is available on the BlueBEAR Job Submission page.
  • BEAR and CaStLeS Cloud VMs: These VMs can have one of two OSes. Those with access to a BEAR Cloud or CaStLeS VM should check that the listed architectures for an application include the OS of VM being used. The VMs, irrespective of OS, will use the haswell CPU type.

Extensions

  • intervals 0.15.2
  • oompaBase 3.2.9
  • oompaData 3.1.1
  • shinycssloaders 1.0.0
  • TailRank 3.2.1

More Information

For more information visit the leafcutter website.

Dependencies

This version of leafcutter has a direct dependency on: DirichletMultinomial/1.32.0-foss-2020a-R-4.0.0 foss/2020a Perl/5.30.2-GCCcore-9.3.0 Python/2.7.18-GCCcore-9.3.0 R/4.0.0-foss-2020a regtools/0.5.2-foss-2020a SAMtools/1.10-GCC-9.3.0

Last modified on 11th March 2021