recipe bioconductor-pdatk

Pancreatic Ductal Adenocarcinoma Tool-Kit

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/PDATK.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-pdatk/meta.yaml

Pancreatic ductal adenocarcinoma (PDA) has a relatively poor prognosis and is one of the most lethal cancers. Molecular classification of gene expression profiles holds the potential to identify meaningful subtypes which can inform therapeutic strategy in the clinical setting. The Pancreatic Cancer Adenocarcinoma Tool-Kit (PDATK) provides an S4 class-based interface for performing unsupervised subtype discovery, cross-cohort meta-clustering, gene-expression-based classification, and subsequent survival analysis to identify prognostically useful subtypes in pancreatic cancer and beyond. Two novel methods, Consensus Subtypes in Pancreatic Cancer (CSPC) and Pancreatic Cancer Overall Survival Predictor (PCOSP) are included for consensus-based meta-clustering and overall-survival prediction, respectively. Additionally, four published subtype classifiers and three published prognostic gene signatures are included to allow users to easily recreate published results, apply existing classifiers to new data, and benchmark the relative performance of new methods. The use of existing Bioconductor classes as input to all PDATK classes and methods enables integration with existing Bioconductor datasets, including the 21 pancreatic cancer patient cohorts available in the MetaGxPancreas data package.

package bioconductor-pdatk

(downloads) docker_bioconductor-pdatk

Versions:

1.6.0-01.2.0-01.0.0-0

Depends:
Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-pdatk

and update with:

conda update bioconductor-pdatk

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-pdatk:<tag>

(see bioconductor-pdatk/tags for valid values for <tag>)

Download stats