https://github.com/greenelab/tdmresults

Scripts and data for re-creating TDM results.
https://github.com/greenelab/tdmresults

dataset gene-expression results supplement

Last synced: about 2 months ago
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Scripts and data for re-creating TDM results.

• Host: GitHub
• URL: https://github.com/greenelab/tdmresults
• Owner: greenelab
• License: bsd-3-clause
• Created: 2015-10-27T13:23:48.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2016-03-16T23:15:30.000Z (almost 9 years ago)
• Last Synced: 2023-10-20T20:05:53.623Z (about 1 year ago)
• Topics: dataset, gene-expression, results, supplement
• Language: R
• Homepage:
• Size: 1.73 MB
• Stars: 8
• Watchers: 4
• Forks: 3
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# TDMresults

[![DOI](https://zenodo.org/badge/doi/10.5281/zenodo.32851.svg)](http://dx.doi.org/10.5281/zenodo.32851)

Scripts and data for re-generating results from the TDM manuscript.

Use run_experiments.R to regenerate the analyses from

[Thompson et al.](https://peerj.com/preprints/1460/).

We are using Git Large File Storage to store gene expression data. You will

need to [install the client](https://git-lfs.github.com/) if you do not already

have it installed. Once you install the client, run `git lfs pull` in the

clone to retrieve the datasets. After retrieving the datasets, using

run_experiments.R will regenerate the results.

This requires the following R & Bioconductor packages be installed (see 

check_installs.R for confirmation of installation):

	* ggplot2

	* reshape2

	* Hmisc

	* data.table

	* scales

	* sdcMicro

	* flexclust

	* fpc

	* corrplot

	* ape

	* cluster

	* plyr

	* dplyr

	* devtools

	* quantro

	* preprocessCore

	* gridExtra

	* huge

	* caret

	* limma

	* glmnet

	* e1071

	* stringr

	* gdata

	* binr

   	* cowplot

One github package is required:

    library("devtools")

    install_github(repo = "quantroSim", username = "stephaniehicks")

We have created an R script which will call 'require' on each of these packages

to make sure they are installed: check_installs.R

By default, all input data is expected to be in this local directory and

normalized data and figure output is within this directory as well. If you'd

like to change this behavior, modify "directories.R".

Acknowledgements:

This research is funded in part by the Gordon and Betty Moore Foundation’s

Data-Driven Discovery Initiative through Grant GBMF4552 to CSG. JT is a Neukom

Graduate Fellow supported by the William H. Neukom 1964 Institute for

Computational Science. This work was supported in part by P20 GM103534,

P30 CA023108 and UL1 TR001086 from the NIH and an American Cancer Society

Research Grant, #IRG-82-003-27. The funders had no role in study design, data

collection and analysis, decision to publish, or preparation of the manuscript.