omiethescientist

scVIDR

Single Cell Variational Inference of the Dose Response (scVIDR) a VAE tool used to predict expression of chemcial perturbations across cell types.

convert_merscope_to_xenium_explorer

export merscope data to xenium explorer directory using sopa tool

DemoTox-PK

DemoToxPK

Interactive Pluto Notebooks For Learning Pharamacokinetics and Toxicodynamics

Differential-Zonation

Differential Zonation is a fork of DryR specifically for calculating differential spatial zonation in the liver lobule.

HVIT

Hyperbolic Variational Autoencoder that uses the Wrapped normal to embed single cell data. This is used to infer hierarchical trajectories in the single cell data.

HyperbolicDeepLearning

A set of hyperbolic deep learning models I can use for research

IDILI

Using toxikinetic/toxicodynamic models to describe the etiology idiosyncratic drug induced liver injury in a quantitative way.

My-Rosalind-Solutions

Github repository of my solutions to the Rosalind problems @ https://rosalind.info

Waddington-Potential-Surface

A desktop repository for the code that numerically integrates the potential function of a theoretical genetic circuit.

omiethescientist/HyperbolicDeepLearning

A set of hyperbolic deep learning models I can use for research

omiethescientist/Differential-Zonation

Differential Zonation is a fork of DryR specifically for calculating differential spatial zonation in the liver lobule.

omiethescientist/convert_merscope_to_xenium_explorer

export merscope data to xenium explorer directory using sopa tool

omiethescientist/DemoTox-PK

omiethescientist/DemoToxPK

Interactive Pluto Notebooks For Learning Pharamacokinetics and Toxicodynamics

omiethescientist/HVIT

Hyperbolic Variational Autoencoder that uses the Wrapped normal to embed single cell data. This is used to infer hierarchical trajectories in the single cell data.

omiethescientist/IDILI

Using toxikinetic/toxicodynamic models to describe the etiology idiosyncratic drug induced liver injury in a quantitative way.

omiethescientist/My-Rosalind-Solutions

Github repository of my solutions to the Rosalind problems @ https://rosalind.info

omiethescientist/Waddington-Potential-Surface

A desktop repository for the code that numerically integrates the potential function of a theoretical genetic circuit.

omiethescientist/merscope_visualize

Visualize MERSCOPE data using spatial-data with napari.

omiethescientist/MSUToxCompBio

Bioinformatics Code for Epigenomic Data

omiethescientist/NonLinDynChaos

Interactive Jupyter Notebooks For Nonlinear Dynamics

omiethescientist/rust-book

My repository for learning rust from "the book"

omiethescientist/tcdd-circadian-zonation

Mixed effects modeling for rhythmic and spatial expression in a single nucleus RNA-seq from the liver of mice acutely treated with TCDD.

omiethescientist/VICPLD

Variational Inference of Combinatorial Peruturbations with Linear Decoders. We utilize ideas from conditional VAEs and linear decoder VAEs to create interpretable factor models of drug perturbations and thus discover genes involved single and combination therapies.