bioconductor-ChAMP

Software Description:

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC.
The ChAMP package is designed for the analysis of Illumina Methylation beadarray data (EPIC and 450k) and provides a pipeline that integrates currently available 450k and EPIC analysis methods. This includes a variety of different data import methods (e.g. from .idat files or a beta-valued matrix) and Quality Control plots. Type-2 probe correction methods include SWAN¹, Peak Based Correction (PBC)² and BMIQ³ (the default choice). The popular Functional Normalization⁴ function offered by the minfi⁵⁶ package is also available. The singular value decomposition (SVD) method⁷ allows an in-depth look at batch effects, and for correction of multiple batch effects the ComBat method⁸ has been implemented. Adjusting for cell-type heterogeneity can be done via RefbaseEWAS⁹. ChAMP also includes a function for infering copy-number alterations from either 450k or EPIC data¹⁰. For the identification of Differentially Methylated Regions (DMR), ChAMP offers the new Probe Lasso method¹¹, in addition to previous DMR detection functions Bumphunter¹² and DMRcate¹³. For users who need to find Differe.

Software Home Page: Bioconductor ChAMP

Software Documentation:

To run this software in a Linux environment on LCC,
run the command(s):

#To load module
module load ccs/conda/bioconductor-champ-2.16.1

#To unload module
conda deactivate