@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 703 177

  2. scihub

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

    Jupyter Notebook 109 17

  3. continuous_analysis

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

    Jupyter Notebook 71 10

  4. TDM

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

    R 17 4

  5. adage-server

    Webserver for ADAGE models.

    JavaScript 5 8

  6. DAPS

    Denoising Autoencoders for Phenotype Stratification

    HTML 29 6

  • The manuscript bot for automated scholarly publishing (Python package)

    Python 25 8 Updated Oct 19, 2018
  • Python 3 BSD-3-Clause Updated Oct 19, 2018
  • An application that is responsive to CZI's RFA.

    CSS 1 Updated Oct 19, 2018
  • Manuscript describing open collaborative writing with Manubot

    Jupyter Notebook 5 6 Updated Oct 19, 2018
  • Assigning biological knowledge to compressed gene expression features

    Jupyter Notebook 2 Updated Oct 18, 2018
  • Matrix-based storage & computation on hetnets to enable a search engine for hetnets

    Jupyter Notebook 6 5 Updated Oct 16, 2018
  • Building classifiers using cancer transcriptomes across 33 different cancer-types

    Jupyter Notebook 28 9 BSD-3-Clause Updated Oct 15, 2018
  • Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four

    R 6 5 BSD-3-Clause 1 issue needs help Updated Oct 10, 2018
  • Clone me to create your manuscript

    CSS 96 24 Updated Oct 9, 2018
  • Extracting when a compound treats a disease from the literature with Snorkel 🏊

    Jupyter Notebook 9 6 Updated Oct 8, 2018
  • Training and evaluating a variational autoencoder for pan-cancer gene expression data

    Jupyter Notebook 51 17 BSD-3-Clause Updated Oct 3, 2018
  • To explore the use of latent space transformations using pseudomonas transcriptomic data.

    Jupyter Notebook 1 BSD-3-Clause Updated Oct 3, 2018
  • Download metadata for all DOIs using the Crossref API

    Jupyter Notebook 14 5 Updated Sep 25, 2018
  • Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models

    HTML 5 5 Updated Sep 14, 2018
  • A unsupervised transfer learning approach for rare disease transcriptomics

    HTML 7 1 Updated Aug 22, 2018
  • R 1 1 Updated Aug 16, 2018
  • A collaboratively written review paper on deep learning, genomics, and precision medicine

    CSS 703 177 1 issue needs help Updated Aug 15, 2018
  • Case-control genetics datasets evolved to be epistatic

    PostScript 2 1 Updated Aug 15, 2018
  • A repository that collects our findings from our efforts under the CZI/HCA project.

    CSS 1 1 Updated Aug 11, 2018
  • Shared Latent Space VAE's

    Python 1 1 Updated Aug 10, 2018
  • R 1 2 Updated Aug 6, 2018
  • Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs

    Python 6 3 MIT Updated Aug 3, 2018
  • Privacy-preserving generative deep neural networks support clinical data sharing

    Jupyter Notebook 43 15 Updated Jul 2, 2018
  • R package for normalizing RNA-seq data to make them comparable to microarray data.

    R 17 4 BSD-3-Clause Updated Jun 25, 2018
  • Continuous administration of the Greene Lab's electronic scrum

    Python 7 3 Updated Jun 22, 2018
  • Webserver for ADAGE models.

    JavaScript 5 8 1 issue needs help Updated Jun 8, 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 5 2 BSD-3-Clause Updated Jun 6, 2018
  • Source code and data analyses for the Sci-Hub Coverage Study

    Jupyter Notebook 109 17 Updated May 18, 2018
  • a port of Ghost's casper theme for Hugo

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

    4 7 CC0-1.0 Updated May 8, 2018