@greenelab

Greene Laboratory

Greene Laboratory at the University of Pennsylvania

Pinned repositories

  1. deep-review

    A collaboratively written review paper on deep learning, genomics, and precision medicine

    CSS 414 124

  2. scihub

    Source code and data analyses for the Sci-Hub Coverage Study

    Jupyter Notebook 67 9

  3. continuous_analysis

    Computational reproducibility using Continuous Integration to produce verifiable end-to-end runs of scientific analysis.

    Jupyter Notebook 58 8

  4. TDM

    R package for normalizing RNA-seq data to make them comparable to microarray data.

    R 13 2

  5. adage-server

    Webserver for ADAGE models.

    JavaScript 4 8

  6. DAPS

    Denoising Autoencoders for Phenotype Stratification

    HTML 26 5

  • A collaboratively written review paper on deep learning, genomics, and precision medicine

    CSS 414 124 Updated Jan 18, 2018
  • Webserver for ADAGE models.

    JavaScript 4 8 1 issue needs help Updated Jan 17, 2018
  • Manuscript for the Sci-Hub Coverage Study

    CSS 12 6 CC-BY-4.0 Updated Jan 18, 2018
  • Source code and data analyses for the Sci-Hub Coverage Study

    Jupyter Notebook 67 9 Updated Jan 17, 2018
  • Collecting data on whether library access to scholarly literature

    Jupyter Notebook 1 2 Updated Jan 17, 2018
  • Extracting when a compound treats a disease from the literature with Snorkel ๐ŸŠ

    Jupyter Notebook 4 3 Updated Jan 17, 2018
  • The manuscript bot for automated scholarly publishing

    Python 6 4 Updated Jan 17, 2018
  • Building classifiers using cancer transcriptomes across 33 different cancer-types

    Jupyter Notebook 5 2 BSD-3-Clause Updated Jan 17, 2018
  • Materials for GCB535 at Penn.

    Jupyter Notebook 11 1 BSD-3-Clause Updated Jan 17, 2018
  • Clone me to create your manuscript

    CSS 36 13 Updated Jan 16, 2018
  • Onboarding materials for the Greene Lab

    3 CC0-1.0 Updated Jan 16, 2018
  • Overrepresentation analysis for KEGG and PID pathways using community detection

    Python 2 2 BSD-3-Clause Updated Jan 7, 2018
  • This repository is in support of the PathCORE-T paper (https://doi.org/10.1101/147645). It contains all the code and necessary data/metadata to repeat all analyses in the paper.

    Jupyter Notebook 1 1 BSD-3-Clause Updated Jan 5, 2018
  • R 1 Updated Dec 22, 2017
  • Manubot 2018 development proposal

    CSS Updated Dec 22, 2017
  • Python 3 BSD-3-Clause Updated Dec 19, 2017
  • Python 2 1 Updated Dec 18, 2017
  • Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

    HTML 1 Updated Dec 15, 2017
  • d3-based gene network visualization

    JavaScript 2 Updated Dec 14, 2017
  • Python 1 2 BSD-3-Clause Updated Dec 4, 2017
  • Training and evaluating a variational autoencoder for pan-cancer gene expression data

    Jupyter Notebook 17 4 BSD-3-Clause Updated Nov 30, 2017
  • Privacy-preserving generative deep neural networks support clinical data sharing

    Jupyter Notebook 13 4 Updated Nov 15, 2017
  • Data for the Sci-Hub Stats Browser

    Jupyter Notebook 1 Updated Nov 7, 2017
  • Manuscript describing the Deep Review Collaborative Workflow and Manubot System

    Jupyter Notebook 1 3 CC-BY-4.0 Updated Nov 2, 2017
  • Python 2 BSD-3-Clause Updated Nov 2, 2017
  • Scripts to automate deployment of an adage-server instance

    Shell 3 Updated Oct 31, 2017
  • Shell 1 Updated Oct 30, 2017
  • Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four

    R 4 4 BSD-3-Clause 1 issue needs help Updated Oct 27, 2017
  • R 6 3 BSD-3-Clause Updated Oct 18, 2017
  • Methods to build a network of pathway co-occurrence relationships out of expression signatures extracted from transcriptomic compendia.

    Python 2 2 BSD-3-Clause Updated Oct 17, 2017