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https://github.com/broadinstitute/dlbcl_nat_med_april_2018

https://github.com/broadinstitute/dlbcl_nat_med_april_2018

Science Score: 26.0%

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    Found 4 DOI reference(s) in README
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Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: broadinstitute
  • Language: R
  • Default Branch: master
  • Size: 60.5 MB
Statistics
  • Stars: 14
  • Watchers: 36
  • Forks: 7
  • Open Issues: 0
  • Releases: 0
Created over 8 years ago · Last pushed about 6 years ago
Metadata Files
Readme

README.md

This repository contains instructions on how to build and run a docker image containing the scripts used to generate clusters used to identify DLBCL subtypes in the publication:

Chapuy, Stewart, & Dunford et al. "Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes." Nature Medicine, 30 April 2018. https://doi.org/10.1038/s41591-018-0016-8

Based on a modified consensus clustering algorithm first applied to expression data in the publication:

Brunet et al. "Metagenes and molecular pattern discovery using matrix factorization." PNAS March 23, 2004. 101 (12) 4164-4169; https://doi.org/10.1073/pnas.0308531101

Please cite both publications if referring to this work.

To run the module, first CD into the 'consensus_clustering' directory and build the docker container using the Dockerfile there:

cd consensusclustering docker build . -t dlbclconsensus_clustering

Then run the provided wrapper script in the docker container using the following command:

docker run --mount type=bind,source=${PWD}/inputdata,target=/Rscripts/inputdata --mount type=bind,source=${PWD}/outputdir,target=/Rscripts/outputdir dlbclconsensusclustering Rscript runconsensusclustering.R

Owner

  • Name: Broad Institute
  • Login: broadinstitute
  • Kind: organization
  • Location: Cambridge, MA

Broad Institute of MIT and Harvard

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Dependencies

consensus_clustering/src/GDAC_TopgenesforCluster/impute/DESCRIPTION cran
  • R >= 1.7.0 depends
consensus_clustering/Dockerfile docker
  • debian jessie build