Greene Laboratory

Repositories

• covid19-review

  A collaborative review of the emerging COVID-19 literature. Join the chat here:

  review manuscript manubot covid-19 sars-cov-2
  HTML 66 79 264 (3 issues need help) 3 Updated Sep 20, 2020

• annorxiver-journal-recommender

  A web app that uses machine learning to recommend the most suitable journals based on the text content of your preprint

  nlp web-app journals nlp-machine-learning
  JavaScript 2 2 1 1 Updated Sep 18, 2020

• generic-expression-patterns
  Jupyter Notebook BSD-3-Clause 1 1 7 1 Updated Sep 18, 2020

• eslint-config-greenelab

  ESLint config for React applications
  JavaScript 0 0 0 0 Updated Sep 18, 2020

• greenelab.com

  The website source code for greenelab.com

  jekyll website lab
  HTML 7 1 1 1 Updated Sep 18, 2020

• pancancer-evaluation

  Evaluating genome-wide prediction of driver mutations using pan-cancer data
  Jupyter Notebook BSD-3-Clause 1 0 10 1 Updated Sep 18, 2020

• labsite-rootstock

  A customizable, flexible template for lab websites. Includes automatic citations, GitHub tag imports, and more.
  0 0 0 0 Updated Sep 18, 2020

• annorxiver

  Annotating Rxiv preprints in an automated fashion
  Jupyter Notebook 3 3 1 2 Updated Sep 17, 2020

• onboarding

  Onboarding materials for the Greene Lab

  lab greenelab onboarding guidelines upenn lab-carpentry
  CC0-1.0 12 19 1 1 Updated Sep 17, 2020

• simulate-expression-compendia

  Software to simulate gene expression compendia.
  Jupyter Notebook BSD-3-Clause 3 4 1 0 Updated Sep 16, 2020

• saged

  Semi-supervised Analysis of Gene Expression Data
  Jupyter Notebook BSD-3-Clause 1 1 2 0 Updated Sep 15, 2020

• annorxiver_manuscript

  This manuscript covers the annorxiver project.
  HTML 2 1 0 0 Updated Sep 14, 2020

• adage-frontend

  The Adage web app, a tool to explore gene expression data and discover new insights from machine learning models

  science machine-learning bioinformatics research genomics web-app gene-expression
  JavaScript 1 2 2 2 Updated Sep 12, 2020

• connectivity-search-manuscript

  Manuscript describing Hetnet Connectivity Search

  networks manuscript hetnets hetnet-connecivity-search dwpcs
  HTML 3 4 2 0 Updated Sep 11, 2020

• brand

  Logos and other brand assets for the Greene Lab organization
  0 0 0 0 Updated Sep 11, 2020

• assets

  Assets (logos, icons, animations, sounds, etc) for use in the Greene Lab

  icons lab logos
  0 0 0 0 Updated Sep 9, 2020

• deep-review

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

  review deep-learning genomics neural-networks manuscript manubot
  HTML 260 1,101 417 (1 issue needs help) 2 Updated Sep 9, 2020

• scihub

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

  data-science doi open-data journals scopus libgen crossref
  Jupyter Notebook 30 189 8 6 Updated Sep 9, 2020

• tribe

  An open-source webserver that allows for easy, reproducible genomics analyses between different webservers
  Python 3 1 12 3 Updated Sep 5, 2020

• compbio-edi

  Curated summary of efforts to promote equity, diversity, and inclusion in computational biology PhD programs and societies.
  4 1 0 0 Updated Sep 4, 2020

• iscb-diversity-manuscript

  Analysis of ISCB Fellows and Keynotes Reveals Disparities

  diversity bioinformatics manuscript iscb manubot
  HTML 4 3 1 0 Updated Sep 3, 2020

• BioBombe

  BioBombe: Sequentially compressed gene expression features enhances biological signatures

  gene-sets compression network tcga gene-expression autoencoder hetnet
  Jupyter Notebook 13 35 0 0 Updated Sep 2, 2020

• iscb-diversity

  Analyzing diversity of ISCB keynote speakers & fellows compared to the field of bioinformatics

  diversity bioinformatics computational-biology pubmed iscb keynotes ismb
  1 package Jupyter Notebook 0 6 2 0 Updated Aug 24, 2020

• connectivity-search-backend

  Django backend for hetnet connectivity search

  django database backend hetio hetmech hetnets hetnet-connectivity-search
  Python 2 5 7 0 Updated Aug 8, 2020

• wiki-nationality-estimate

  Name-based nationality prediction trained on Wikipedia

  machine-learning wikipedia nationalize
  Python 1 3 3 0 Updated Aug 7, 2020

• core-accessory-interactome
  Jupyter Notebook BSD-3-Clause 1 0 2 0 Updated Aug 7, 2020

• pubtator

  Retrieve and process PubTator annotations

  nlp data text-mining pubmed snorkel pubtator
  Python 8 18 3 0 Updated Aug 6, 2020

• scrumlord

  Continuous administration of the Greene Lab's electronic scrum

  administration cron travis-ci scrum continuous
  Python 6 10 2 0 Updated Aug 4, 2020

• ponyo
  Jupyter Notebook BSD-3-Clause 2 0 0 0 Updated Jul 17, 2020

• hetmech

  Prototyping DWPC p-values for detecting hetnet connectivity

  numpy matrix scipy hetionet hetnet networks mechanism
  Jupyter Notebook 6 7 7 2 Updated Jul 13, 2020