dohlee

metheor

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

chromoformer

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

antiberty-pytorch

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

snakemake-wrappers

:snake: Snakemake wrappers for bioinformatics.

spliceai-pytorch

Implementation of SpliceAI, Illumina's deep neural network to predict variant effects on splicing, in PyTorch.

foldingdiff-pytorch

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

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.

pifold-pytorch

An unofficial re-implementation of PiFold, a fast inverse-folding algorithm for protein sequence design, in PyTorch.

rasp-pytorch

Reimplementation of RaSP, a deep neural network for rapid protein stability prediction, in PyTorch.

rosettafold-pytorch

An unofficial re-implementation of RoseTTAFold, a three-track deep learning model for protein structure prediction.

snakemake-cartesian-ddg

Snakemake pipeline for Rosetta 'cartesian-ddg' protocol for protein stability prediction upon mutations.

diffab-pytorch

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

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"

protein-structure-preprocessing

Automated pipeline for preparing protein structure dataset only from a list of PDB ids.

proteinbert-pytorch

Implementation of ProteinBERT, a deep language model designed for proteins.

protstruc

Protein structure handling in Python made easy.

bpnet-pytorch

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

deepab-pytorch

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

dohlee.github.io

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

eve-pytorch

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

igfold-pytorch

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

snakemake-bismark-methyldackel-sra

Process SRA bisulfite sequencing data easily with Bismark-MethylDackel pipeline.

tranception-pytorch

Implementation of Tranception, a SOTA transformer model for protein fitness prediction, in PyTorch.

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"

meth-ising

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

python-biopipe

samsung-ai-challenge-solution

⚗️ Samsung AI Challenge for Scientific Discovery 5위 솔루션입니다.

snakemake-ngs-qc-summary

Easily get an Excel sheet summarizing QC results for raw sequencing data.

utterances