@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 622 166

  2. scihub

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

    Jupyter Notebook 96 18

  3. continuous_analysis

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

    Jupyter Notebook 67 9

  4. TDM

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

    R 15 3

  5. adage-server

    Webserver for ADAGE models.

    JavaScript 5 8

  6. DAPS

    Denoising Autoencoders for Phenotype Stratification

    HTML 29 6

  • A search engine for hetnets. Matrix implementations of path-count-based measures

    Jupyter Notebook 6 5 Updated Jun 18, 2018
  • Manuscript describing the Deep Review Collaborative Workflow and Manubot System

    Jupyter Notebook 1 4 Updated Jun 18, 2018
  • Clone me to create your manuscript

    CSS 77 22 Updated Jun 18, 2018
  • Assigning biological knowledge to compressed gene expression features

    Jupyter Notebook 1 Updated Jun 17, 2018
  • A repository that collects our findings from our efforts under the CZI/HCA project.

    CSS 1 1 Updated Jun 15, 2018
  • R 1 Updated Jun 10, 2018
  • Webserver for ADAGE models.

    JavaScript 5 8 1 issue needs help Updated Jun 8, 2018
  • Extracting when a compound treats a disease from the literature with Snorkel 🏊

    Jupyter Notebook 8 6 Updated Jun 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 Jun 6, 2018
  • Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

    HTML 1 4 Updated Jun 5, 2018
  • The manuscript bot for automated scholarly publishing

    Python 9 6 Updated Jun 3, 2018
  • Shared Latent Space VAE's

    Python 1 Updated May 31, 2018
  • Source code and data analyses for the Sci-Hub Coverage Study

    Jupyter Notebook 96 18 Updated May 18, 2018
  • Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

    Python 4 2 MIT Updated May 18, 2018
  • 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 May 17, 2018
  • a port of Ghost's casper theme for Hugo

    CSS 7 MIT Updated May 15, 2018
  • Onboarding materials for the Greene Lab

    3 7 CC0-1.0 Updated May 8, 2018
  • Training and evaluating a variational autoencoder for pan-cancer gene expression data

    Jupyter Notebook 46 12 BSD-3-Clause Updated May 7, 2018
  • Python 3 BSD-3-Clause Updated May 7, 2018
  • R 2 Updated Apr 27, 2018
  • Building classifiers using cancer transcriptomes across 33 different cancer-types

    Jupyter Notebook 20 7 BSD-3-Clause Updated Apr 18, 2018
  • A collaboratively written review paper on deep learning, genomics, and precision medicine

    CSS 622 166 1 issue needs help Updated Apr 9, 2018
  • Materials for GCB535 at Penn.

    Jupyter Notebook 11 1 BSD-3-Clause Updated Apr 7, 2018
  • Collecting data on whether library access to scholarly literature

    Jupyter Notebook 3 3 Updated Mar 14, 2018
  • Manuscript for the Sci-Hub Coverage Study

    CSS 15 14 Updated Feb 18, 2018
  • Download metadata for all DOIs using the Crossref API

    Jupyter Notebook 12 4 Updated Feb 7, 2018
  • Downloading and processing pipelines used for single cell gene expression assays of human tumor biopsies

    Shell 1 Updated Jan 25, 2018
  • Overrepresentation analysis for KEGG and PID pathways using community detection

    Python 3 2 BSD-3-Clause Updated Jan 6, 2018
  • Manubot 2018 development proposal

    CSS Updated Dec 22, 2017
  • Python 2 1 Updated Dec 18, 2017