A search engine for hetnets. Matrix implementations of path-count-based measures
Manuscript describing the Deep Review Collaborative Workflow and Manubot System
Clone me to create your manuscript
Assigning biological knowledge to compressed gene expression features
A repository that collects our findings from our efforts under the CZI/HCA project.
Webserver for ADAGE models.
Extracting when a compound treats a disease from the literature with Snorkel
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.
Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models
The manuscript bot for automated scholarly publishing
Shared Latent Space VAE's
Source code and data analyses for the Sci-Hub Coverage Study
Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs
Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four
a port of Ghost's casper theme for Hugo
Onboarding materials for the Greene Lab
Training and evaluating a variational autoencoder for pan-cancer gene expression data
Building classifiers using cancer transcriptomes across 33 different cancer-types
A collaboratively written review paper on deep learning, genomics, and precision medicine
Materials for GCB535 at Penn.
Collecting data on whether library access to scholarly literature
Manuscript for the Sci-Hub Coverage Study
Download metadata for all DOIs using the Crossref API
Downloading and processing pipelines used for single cell gene expression assays of human tumor biopsies
Overrepresentation analysis for KEGG and PID pathways using community detection
Manubot 2018 development proposal