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abyssal-pytorch

Implementation of Abyssal, a deep neural network trained with a new "mega" dataset to predict the impact of an amino acid variant on protein stability.

adipogenesis-methylation

💻 Analysis codes and bioinformatic pipelines for paper "Targeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation" (Park et al., Nature Metabolism. 2022)

antiberty-pytorch

An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.

bioinformatics-one-liners

:memo: Useful bioinformatics one-line commands.

bpnet-pytorch

Implementation of BPNet, a base-resolution convolutional neural network for transcription-factor binding prediction, in PyTorch.

chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

circleci-101

daily-rosalind

:white_check_mark: Solve one rosalind problem per day.

deepab-pytorch

An unofficial re-implementation of DeepAb, an interpretable deep learning model for antibody structure prediction.

deepcpg-pytorch

deeplearning-earlystopping

A minimal python class implementation for early stopping during deep learning model training.

deg-pipeline

diffab-pytorch

An unofficial re-implementation of DiffAb, a diffusion-based generative model for antigen-specific antibody design and optimization.

dirichlet-process

Python implementation for nonparametric bayesian clustering with dirichlet process.

dnmt3a-instability-and-methylation-disorder

💻 Analysis codes and bioinformatics pipelines for paper "Increased local DNA methylation disorder in AMLs with DNMT3A-destabilizing variants and its clinical implication"

dohlee.github.io

A beautiful, simple, clean, and responsive Jekyll theme for academics

dotfiles

eve-pytorch

Implementation of evolutionary model of variant effect (EVE), a deep generative model of evolutionary data, in PyTorch.

foldingdiff-pytorch

An unofficial re-implementation of FoldingDiff, a diffusion-based generative model for protein backbone structure generation.

genomepy

Download genomes the easy way.

geodiff-pytorch

Implementation of GeoDiff, a geometric diffusion model for molecular conformation generation, in PyTorch.

hiv1-rloop

💻 Analysis codes and bioinformatic pipelines for paper "HIV-1-induced host genomic R-loops dictate HIV-1 integration site selection"

idat2beta

Small minfi wrapper to convert IDAT files to beta values.

igfold-pytorch

Unofficial re-implementation of IgFold, a fast antibody structure prediction method, in PyTorch.

julia-ml

Machine learning in julia.

learn-sed

:pencil2: SED tutorial

meth-ising

Fitting 5-parameter 1D Ising models for regionwise information-theoretic properties of DNA methylation states. Implemented in Rust.

meth-pops

Python tool for visualizing methylation status as lollipop diagram.

metheor

:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

methylome-tools

Tutorials for DNA methylome analysis tools