(DRExM³L) Drug REpurposing using eXplainable Machine Learning and Mechanistic Models of signal transduction

Simplify functional enrichment results

Profile RNA-seq data using published TB gene signatures

A unified multi-task learning framework for prediction of individualized tissue gene expression profiles.

Supervised Negative Binomial NMF for Mutational Signature Discovery

Dose-L1000 database

Source code for "A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities"

Examples of building and running BVBRC CLI in containers

This repository hosts scripts necessary for the AMD GPU computation demonstration

A Curated List of Computational Biology Datasets Suitable for Machine Learning

scikit-learn: machine learning in Python

Bayesian Aggregation in Genomic applications: a Bayesian latent variable approach for rank aggregation of partial and top ranked lists

Repository with basic information about Rank Aggregation Problem.

Docs and implementation of the reMarkable file sync API

Sync papers from Zotero to a reMarkable tablet

Successful Job Applications and Grants

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

Software to distinguish between common and experiment-specific gene expression signals

Python package to load and query ARCHS4 data

A microbial signatures database

Repository containing notebook with loss functions

Data, results, and code accompanying the manuscript: "Supervised learning is an accurate method for network-based gene classification"

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations