ChAMP 2.18.3-foss-2020a-R-4.0.0

The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.

Accessing ChAMP 2.18.3-foss-2020a-R-4.0.0

To load the module for ChAMP 2.18.3-foss-2020a-R-4.0.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs, and CaStLeS VMs):

module load ChAMP/2.18.3-foss-2020a-R-4.0.0

BEAR Apps Version

2020b

Extensions

  • bsseq 1.24.4
  • ChAMP 2.18.3
  • ChAMPdata 2.20.0
  • DMRcate 2.2.3
  • DSS 2.36.0
  • Illumina450ProbeVariants.db 1.24.0
  • IRanges 2.22.2
  • isva 1.9
  • JADE-2.0-3
  • kpmt 0.1.0
  • missMethyl 1.22.0
  • prettydoc 0.4.1
  • ROC 1.64.0
  • RPMM 1.25
  • ruv 0.9.7.1
  • wateRmelon 1.32.0

More Information

For more information visit the ChAMP website.

Dependencies

This version of ChAMP has a direct dependency on: foss/2020a R/4.0.0-foss-2020a R-bundle-Bioconductor/3.11-foss-2020a-R-4.0.0

Required By

This version of ChAMP is a direct dependent of: BEAR-R-bio/2020a-foss-2020a-R-4.0.0

Last modified on 28th October 2022