An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays
Year: 2018
Type: article
Abstract: Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infinium DNA methylation arrays have been shown to detect copy number alterations at comparable sensitivity. Here we present an accessible, interactive GenePattern notebook for the analysis of copy number variation using Illumina Infinium DNA methylation arrays. The notebook provides a graphical user interface to a workflow using the R/Bioconductor packages minfi and conumee . The environment allows analysis to be performed without the installation of the R software environment, the packages and dependencies, and without the need to write or manipulate code.
Source: F1000Research
Authors: Clarence K. Mah, Jill P. Mesirov, Lukas Chavez
Institutions: University of California San Diego, Moores Cancer Center
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $1,350
Awards: The Integrative Genomics Viewer (IGV): visualization supporting cancer research, GenomeSpace: community web environment for analysis across diverse genomic tools, GenePattern Notebooks for Cancer Research, Embryonal Brain Tumor Networks, Genomic Analysis of Medulloblastomas, Supporting Integrative Genomic Analysis Users with GenePattern
OpenAlex ID: W2902498739