@greenelab

Greene Laboratory

Greene Laboratory at the University of Pennsylvania

  • JavaScript 3 5 Updated Feb 22, 2017
  • Building classifiers using cancer transcriptomes across 33 different cancer-types

    classifier cancer tcga gene-expression transcriptome pancancer

    Python 1 Updated Feb 22, 2017
  • Retrieve and process PubTator annotations

    nlp data text-mining pubmed snorkel pubtator

    Python 3 Updated Feb 22, 2017
  • Materials for GCB535 at Penn.

    Jupyter Notebook 7 Updated Feb 20, 2017
  • A collaboratively written review paper on deep learning, genomics, and precision medicine

    Python 97 29 Updated Feb 18, 2017
  • This repository is the home to ADAGEpath R package

    R 1 Updated Feb 17, 2017
  • Extracting when a compound treats a disease from the literature with Snorkel ๐ŸŠ

    nlp machine-learning hetnet snorkel

    Jupyter Notebook 3 Updated Feb 17, 2017
  • Rigor, Reproducibility, Transparency, and Reagent Validity for Computational Biologists

    HTML 2 6 Updated Feb 5, 2017
  • R Updated Jan 30, 2017
  • Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

    Python 1 1 Updated Jan 20, 2017
  • DEPRECATED: Integrating topologically associating domains (TADs) to prioritize GWAS signal

    Python 1 1 Updated Jan 5, 2017
  • Validating glioblastoma immune cell immunohistochemsitry using computational deconvolution of TCGA tumors

    R 1 Updated Jan 5, 2017
  • Continuous Analysis Example - Performing Differential Expression Analysis with Custom Chip Description Files (CustomCDF)

    R Updated Dec 21, 2016
  • Using Machine Learning to Identify Glioblastoma patients with NF1 inactivation

    Python 4 2 Updated Dec 19, 2016
  • Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.

    Jupyter Notebook 25 1 Updated Nov 28, 2016
  • Stability NMF

    Python 4 1 Updated Nov 23, 2016
  • Scripts to automate deployment of an adage-server instance

    Shell Updated Oct 25, 2016
  • Biological ontologies as hetnets in Neo4j

    Shell Updated Sep 23, 2016
  • Three subtypes of HGSC subtypes fit the data better than four

    machine-learning cancer gene-expression subtype ovarian-cancer

    R 3 3 Updated Sep 7, 2016
  • Example of how continuous analysis can be used for RNA-Seq differential expression.

    R Updated Aug 19, 2016
  • A simple phylogenetic tree building example of Continuous Analysis

    Shell Updated Aug 19, 2016
  • Denoising Autoencoders for Phenotype Stratification

    HTML 16 4 Updated Aug 19, 2016
  • Case-control genetics datasets evolved to be epistatic

    PostScript 1 1 Updated Jul 19, 2016
  • This is the repository for ADAGE (Analysis using Denoising Autoencoders for Gene Expression)

    Python 29 15 Updated May 25, 2016
  • We play a prediction game in our GCB 535 class. The class aims to teach students, primarily biologists, about machine learning methods and their use. This repository hosts the challenge for individuals outside of our lab.

    Python 6 2 Updated Apr 8, 2016
  • Scripts and data for re-creating TDM results.

    R 3 3 Updated Mar 16, 2016
  • R package for normalizing RNA-seq data to make them comparable to microarray data.

    R 8 1 Updated Mar 14, 2016
  • Repository associated with Song et al. manuscript describing a Network-wide Association Study of ADNI Cohorts.

    Python 1 2 Updated Jan 14, 2016
  • Source code associated with "Leveraging global gene expression patterns to predict expression of unmeasured genes"

    R 2 Updated Dec 9, 2015