BiocManager::install("waldronlab/MultiAssayWorkshop", dependencies=TRUE, build_vignettes=TRUE)
Marcel Ramos, Ludwig Geistlinger, and Levi Waldron
CUNY School of Public Health
55 West 125th Street
New York, NY 10027
This workshop demonstrates the leveraging of public multi-omics databases, such as cBioPortal and The Cancer Genome Atlas (TCGA), through the use of the cBioPortalData
and curatedTCGAData
experiment data packages. It provides users with the basics of data management, using the MultiAssayExperiment
data class and the TCGAutils
utility package, and example analyses of multiple assays associated with a single set of biological specimens. In addition to providing a basic overview of key data classes, such as MultiAssayExperiment
and RaggedExperiment
, this workshop intends to provide an overview of cBioPortalData
and curatedTCGAData
experiment data packages and TCGAutils
functionality aimed at enhancing the ease-of-use of TCGA data.
Participants will have a chance to build a MultiAssayExperiment
object from scratch, and will also work with data and interfaces from the the curatedTCGAData
and cBioPortalData
packages.
55 minutes total
Activity | Time |
---|---|
Overview of key packages and data classes | 15m |
Building a MultiAssayExperiment from scratch |
10m |
Introduction to curatedTCGAData , cBioPortalData , and TCGAutils
|
10m |
Creating and importing TCGA multi-assay datasets | 10m |
Subsetting and reshaping multi-assay data | 10m |
TCGAutils
for the management and coordination of multi-omic datacBioPortalData
and curatedTCGAData
For more involved / detailed questions, comments, or bug reports, resort to the Bioconductor support site or create an issue on the MultiAssayExperiment
issue tracker on GitHub.