Gitter Lab

nn4dms

Neural networks for deep mutational scanning data

metl

Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models

LPWC

Lag Penalized Weighted Correlation for Time Series Clustering

ssps

Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference

metl-pretrained

Pretrained METL models with minimal dependencies

ml4bio

A graphical interface for sklearn classification to introduce machine learning to biologists

prmf

Pathway-Regularized Matrix Factorization

SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data

metl-sim

High-throughput framework for running molecular simulations for METL

pria_lifechem

Virtual screening on PriA-SSB and RMI-FANCM with the LifeChem library

pria-ams-enamine

Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries

t-cell-classification

Jupyter notebooks demonstrating a microscopy machine learning image analysis workflow

metl-pub

Supplementary datasets and scripts for the METL manuscript

active-learning-drug-discovery

End-to-end active learning pipeline for virtual screening and drug discovery

pathway-parameter-advising

Parameter advising for biological pathway creation algorithms

hiv1-aurkb

Scripts for analyzing HIV-1 producer cell proteomic and phosphoproteomic data

min-cost-flow

Pathway reconstruction with a minimum cost flow algorithm

network-notebook-examples

Test pandas and networkx in Jupyter notebooks

pathway-localization

Scripts, data, and supplementary information for "Graph algorithms for predicting subcellular localization at the pathway level"

pharmaco-image

SINGE-supplemental

Supplemental scripts and analyses for the SINGE manuscript

NetworkMeasures

bds-srop-demo-manuscript

Demo manubot manuscript for BDS SROP students

influenza-pb2

Analysis of influenza PB2 protein interactions

LPWC-examples

Examples for running LPWC that are executable within Binder

ml-bio-workshop

Former repository for the Machine Learning for Biology workshop. Moved to https://github.com/carpentries-incubator/ml4bio-workshop.

osmotic-stress

A study of yeast osmotic stress response signaling

sim-path

Improving subnetwork identification with pathway-based simulation

test-notifications

Test repo for notification integration

tps

Temporal Pathway Synthesizer