Greene Laboratory

Repositories

• saged

  Semi-supervised Analysis of Gene Expression Data

  machine-learning analysis tool gene-expression
  Jupyter Notebook BSD-3-Clause 1 2 4 1 Updated Nov 27, 2020

• ponyo

  Software to simulate compendium-wide gene expression data using a VAE.

  machine-learning neural-network gene-expression software autoencoder data-simulation variational-autoencoder
  Jupyter Notebook BSD-3-Clause 2 0 2 1 Updated Nov 25, 2020

• hclust

  Agglomerative hierarchical clustering in JavaScript

  javascript package node math clustering hierarchical-clustering agglomerative-clustering
  JavaScript MIT 0 3 0 0 Updated Nov 25, 2020

• greenelab.com

  The website source code for greenelab.com

  jekyll website lab greenelab
  HTML 2 0 0 0 Updated Nov 25, 2020

• lab-website-template

  (Pre-release) An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more

  jekyll template website
  HTML 3 16 3 0 Updated Nov 25, 2020

• covid19-review

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

  review virus immunology manuscript hacktoberfest manubot covid-19
  HTML 68 88 269 (3 issues need help) 1 Updated Nov 25, 2020

• annorxiver

  Annotating Rxiv preprints in an automated fashion

  machine-learning publishing biorxiv preprints medrxiv
  Jupyter Notebook 3 3 1 1 Updated Nov 24, 2020

• annorxiver_manuscript

  This manuscript covers the annorxiver project.

  publishing open-science biorxiv preprints manuscript manubot medrxiv
  HTML 2 1 0 0 Updated Nov 24, 2020

• iscb-diversity

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

  diversity bioinformatics computational-biology pubmed iscb keynotes ismb
  2 packages Jupyter Notebook 0 6 2 0 Updated Nov 23, 2020

• preprint-similarity-search

  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 1 2 1 0 Updated Nov 20, 2020

• generic-expression-patterns

  Distinguishing between generic and experiment-specific gene expression signals.

  machine-learning neural-network analysis gene-expression software autoencoder variational-autoencoder
  Jupyter Notebook BSD-3-Clause 1 1 7 0 Updated Nov 20, 2020

• simulate-expression-compendia

  Evaluating the effect of technical sources of variability in large-scale gene expression compendia.

  analysis tool dataset software methodology supplement
  Jupyter Notebook BSD-3-Clause 3 4 1 0 Updated Nov 20, 2020

• pancancer-evaluation

  Evaluating genome-wide prediction of driver mutations using pan-cancer data

  classifier machine-learning genome analysis cancer gene-expression pancancer
  Jupyter Notebook BSD-3-Clause 1 2 15 0 Updated Nov 19, 2020

• circadian-clock-modulators

  Network analysis of hits from a screen of circadian clock modulating compounds

  screen circadian-rhythm circadian-medicine
  Jupyter Notebook 0 1 0 1 Updated Nov 18, 2020

• biovectors

  Detecting Biomedical Relationships using Word2vec On Pubtator Central

  nlp machine-learning word2vec
  Python BSD-2-Clause 2 0 0 0 Updated Nov 17, 2020

• onboarding

  Onboarding materials for the Greene Lab

  lab greenelab onboarding guidelines upenn lab-carpentry
  CC0-1.0 13 19 1 1 Updated Nov 12, 2020

• iscb-diversity-manuscript

  Analysis of ISCB Fellows and Keynotes Reveals Disparities

  diversity bioinformatics manuscript iscb manubot
  HTML 5 3 1 0 Updated Nov 10, 2020

• deep-review

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

  review deep-learning genomics neural-networks manuscript manubot
  HTML 262 1,115 419 (1 issue needs help) 2 Updated Nov 10, 2020

• wiki-nationality-estimate

  Name-based nationality prediction trained on Wikipedia

  machine-learning wikipedia nationalize
  Python 1 3 2 1 Updated Oct 29, 2020

• compbio-edi

  Curated summary of efforts to promote equity, diversity, and inclusion in computational biology PhD programs and societies.

  diversity computational-biology phd curation program inclusion
  5 5 0 0 Updated Oct 28, 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 0 2 2 0 Updated Oct 21, 2020

• pubtator

  Retrieve and process PubTator annotations

  nlp data text-mining tool pubmed snorkel pubtator
  Python 9 21 3 0 Updated Oct 15, 2020

• brand

  Logos and other brand assets for the Greene Lab organization

  brand administration lab greenelab
  0 0 0 0 Updated Oct 11, 2020

• LINCS_latent_space

  Training VAE on LINCS dataset.

  gene-expression autoencoder lincs drug variational-autoencoder
  Jupyter Notebook BSD-3-Clause 1 0 1 0 Updated Sep 29, 2020

• eslint-config-greenelab

  ESLint config for React applications

  react javascript config html utility formatting lab
  JavaScript 0 0 0 0 Updated Sep 18, 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

• scihub

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

  data-science doi open-data journals scopus libgen crossref
  Jupyter Notebook 31 194 8 6 Updated Sep 9, 2020

• tribe

  An open-source webserver that allows for easy, reproducible genomics analyses between different webservers

  gene-sets web-server server tool
  Python 3 1 12 3 Updated Sep 5, 2020

• BioBombe

  BioBombe: Sequentially compressed gene expression features enhances biological signatures

  gene-sets compression network tcga gene-expression autoencoder hetnet
  Jupyter Notebook 14 40 0 0 Updated Sep 2, 2020

• connectivity-search-backend

  Django backend for hetnet connectivity search

  django database backend hetio hetmech hetnets hetnet-connectivity-search
  Python 2 6 7 0 Updated Aug 8, 2020