gitter-lab/network-notebook-examples

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Created over 5 years ago
Updated over 1 year ago

gitter-lab/network-notebook-examples

gitter-lab

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Test pandas and networkx in Jupyter notebooks

nn4dms

Neural networks for deep mutational scanning data

Jupyter Notebook

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

prmf

Pathway-Regularized Matrix Factorization

SINGE

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

ml4bio

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

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

Jupyter Notebook

t-cell-classification

Jupyter notebooks demonstrating a microscopy machine learning image analysis workflow

Jupyter Notebook

pria-ams-enamine

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

Jupyter Notebook

metl-pub

Supplementary datasets and scripts for the METL manuscript

pathway-parameter-advising

Parameter advising for biological pathway creation algorithms

active-learning-drug-discovery

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

Jupyter Notebook

SINGE-supplemental

Supplemental scripts and analyses for the SINGE manuscript

hiv1-aurkb

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

min-cost-flow

Pathway reconstruction with a minimum cost flow algorithm

pharmaco-image

Jupyter Notebook

pathway-localization

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