Gitter Lab (@gitter-lab)
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Top repositories

1

nn4dms

Neural networks for deep mutational scanning data
Jupyter Notebook
66
star
2

metl

Mutational Effect Transfer Learning (METL) framework for pretraining and finetuning biophysics-informed protein language models
Python
22
star
3

LPWC

Lag Penalized Weighted Correlation for Time Series Clustering
R
20
star
4

ssps

Sparse Signaling Pathway Sampling: MCMC for signaling pathway inference
Julia
14
star
5

metl-pretrained

Pretrained METL models with minimal dependencies
Python
13
star
6

prmf

Pathway-Regularized Matrix Factorization
Python
11
star
7

SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MATLAB
11
star
8

ml4bio

A graphical interface for sklearn classification to introduce machine learning to biologists
Python
11
star
9

metl-sim

High-throughput framework for running molecular simulations for METL
Python
10
star
10

pria_lifechem

Virtual screening on PriA-SSB and RMI-FANCM with the LifeChem library
Jupyter Notebook
8
star
11

t-cell-classification

Jupyter notebooks demonstrating a microscopy machine learning image analysis workflow
Jupyter Notebook
6
star
12

pria-ams-enamine

Virtual screening on PriA-SSB with the AMS and Enamine REAL libraries
Jupyter Notebook
6
star
13

metl-pub

Supplementary datasets and scripts for the METL manuscript
Python
5
star
14

pathway-parameter-advising

Parameter advising for biological pathway creation algorithms
Python
3
star
15

active-learning-drug-discovery

End-to-end active learning pipeline for virtual screening and drug discovery
Jupyter Notebook
3
star
16

SINGE-supplemental

Supplemental scripts and analyses for the SINGE manuscript
MATLAB
1
star
17

hiv1-aurkb

Scripts for analyzing HIV-1 producer cell proteomic and phosphoproteomic data
Python
1
star
18

min-cost-flow

Pathway reconstruction with a minimum cost flow algorithm
Python
1
star
19

network-notebook-examples

Test pandas and networkx in Jupyter notebooks
Jupyter Notebook
1
star
20

pharmaco-image

Jupyter Notebook
1
star
21

pathway-localization

Scripts, data, and supplementary information for "Graph algorithms for predicting subcellular localization at the pathway level"
Python
1
star