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Matt Hodgman's Projects

aspen icon aspen

A script and supporting files that can construct a tree using the MeSH terms of drugs in ChEMBL.

celluster icon celluster

Consensus clustering from multiple methods used in MCMICRO to cluster cell types.

drugcluster icon drugcluster

Several algorithms to cluster drugs based on their similarity.

drugsimilarity icon drugsimilarity

A python script for comparing drugs based on the semantic distance between the MeSH headings of their ChEMBL indications.

drugstance icon drugstance

Calculate the semantic distance between drugs based on their indications using information theory.

drugvis icon drugvis

Scripts for transforming and visualizing drug similarity and clustering data.

extramponline icon extramponline

An online implementation of the ExtRamp algorithm with user-friendly UI

fiddle icon fiddle

FIDDLE (https://doi.org/10.1093/jamia/ocaa139) edited so that it doesn't throw a specific error I keep getting (see issue #11 on original repo) and defaults with discretize: no

iccm icon iccm

Iterative Combining Clusterings Method (ICCM) implementation in Python

mcmicro icon mcmicro

Multiple-choice microscopy pipeline

proteohist icon proteohist

An AI method for predicting tumor protein expression from H&E histopathology slides

rxrx19adlbatchcorrect icon rxrx19adlbatchcorrect

Python pipeline to identify and remove batch effects in the deep learning embeddings of the RxRx19a dataset and better identify potentially effective compounds against SARS-CoV-2

silhouette icon silhouette

A suite of tools for using silhouette scores to analyze clustering results

umap icon umap

Run UMAP on cellular data from MCMICRO and color based on different clustering algorithm's cluster assignments.

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