inferCNV 1.12.0-foss-2021b-R-4.2.0

InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes.

Accessing inferCNV 1.12.0-foss-2021b-R-4.2.0

To load the module for inferCNV 1.12.0-foss-2021b-R-4.2.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load bear-apps/2021b
module load inferCNV/1.12.0-foss-2021b-R-4.2.0

BEAR Apps Version

2021b

Architectures

EL8-cascadelakeEL8-haswellEL8-icelakeUbuntu20.04-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

  • infercnv 1.12.0
  • parallelDist 0.2.6
  • phyclust-0.1-30

More Information

For more information visit the inferCNV website.

Dependencies

This version of inferCNV has a direct dependency on: foss/2021b Python/3.9.6-GCCcore-11.2.0 R/4.2.0-foss-2021b R-bundle-Bioconductor/3.15-foss-2021b-R-4.2.0 rjags/4-13-foss-2021b-R-4.2.0

Last modified on 21st July 2022