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The manuscript bot for automated scholarly publishing (Python package)
An application that is responsive to CZI's RFA.
Manuscript describing open collaborative writing with Manubot
Assigning biological knowledge to compressed gene expression features
Matrix-based storage & computation on hetnets to enable a search engine for hetnets
Building classifiers using cancer transcriptomes across 33 different cancer-types
Two or three subtypes of high grade serous ovarian cancer subtypes fit data from different populations better than four
Clone me to create your manuscript
Extracting when a compound treats a disease from the literature with Snorkel
Training and evaluating a variational autoencoder for pan-cancer gene expression data
To explore the use of latent space transformations using pseudomonas transcriptomic data.
Download metadata for all DOIs using the Crossref API
Pipeline analysis for whole exome sequencing of pancreatic cancer PDX models
A unsupervised transfer learning approach for rare disease transcriptomics
A collaboratively written review paper on deep learning, genomics, and precision medicine
Case-control genetics datasets evolved to be epistatic
A repository that collects our findings from our efforts under the CZI/HCA project.
Shared Latent Space VAE's
Pipeline to implement a "TAD_Pathways" analysis. Discover candidate genes based on association signals in TADs
Privacy-preserving generative deep neural networks support clinical data sharing
R package for normalizing RNA-seq data to make them comparable to microarray data.
Continuous administration of the Greene Lab's electronic scrum
Webserver for ADAGE models.
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.
Source code and data analyses for the Sci-Hub Coverage Study
a port of Ghost's casper theme for Hugo
Onboarding materials for the Greene Lab