Joel Eliason's repositories
spatialkmeans
Single-cell spatial omics clustering, incorporating the physical distance between cells into the omics distance. This penalizes cells that are further away from being in the same cluster.
AgentNet
Pytorch implementation of AgentNet, which is designed for reveal hidden interactions and predict future dynamics of the unknown complex system.
bioinf593_final_project
Final project for Bioinf 593: ML in Comp Bio
brain_stat_graph
Experiments in statistics of networks, using brain connectivity graphs
scrna_analysis
A repository containing my investigations into single-cell RNAseq analysis, especially as applied to cancer
causality-lab
Causal discovery algorithms and tools for implementing new ones
csbjDeepLearning
Deep Learning Predicts Microbial Interactions from Self-organized Spatiotemporal Patterns
gnn-model-explainer
gnn explainer
HAL
HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs
histocartography
Histocartography is a framework bringing together AI and Digital Pathology
hmmlearn
Hidden Markov Models in Python, with scikit-learn like API
looptimer
Time calculation for loops in R, to get some idea how long I need to wait.
nest-simulator
The NEST simulator
patho-quant-explainer
Code for replicating results presented in the paper: "Quantifying Explainers of Graph Neural Networks in Computational Pathology"
PhysiCell-Studio
PhysiCell Studio is a graphical tool to allow easy editing of a (XML) model, create initial positions of cells, run a simulation, and visualize results. To contribute, fork and make PRs to the development branch.
ppjsdm
Point process joint species distribution models
ppjsdm_on_datasets
Using the ppjsdm package on datasets.
PyCX
PyCX is a Python-based sample code repository for complex systems research and education.
python-glmnet
A python port of the glmnet package for fitting generalized linear models via penalized maximum likelihood.
rgeyer
Simulate Geyer's saturation process. Aimed for multi-variate and multi-scale versions.
rslurm
Submit R code to a Slurm cluster
shiny-reticulate-app
An end-to-end tutorial creating an R Shiny app that uses the reticulate package with Python 3
SpatialPack
Tools for assessment the association between two spatial processes
tissue-structure-modulates-evolution
Code repository associated with the paper "Tissue structure modulates evolution: premalignant sweeps precede neutral expansion"