Dohoon Lee

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.

bioinformatics-one-liners. :memo: Useful bioinformatics one-line commands.

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

dirichlet-process. Python implementation for nonparametric bayesian clustering with dirichlet process.

pysuffixarray. Suffix array implementation written in python

prism. 🔍 Methylation Pattern-based, Reference-free Inference of Subclonal Makeup. (Lee et al., Bioinformatics. 2019)

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.

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

snakemake-hamburger. :snake::hamburger: A beginner's guide to modular snakemake workflows.

snakemake-bismark-methyldackel. Bismark-MethylDackel DNA methylation quantification pipeline in snakemake.

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

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

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

snakemake-star-rsem. STAR-RSEM pipeline in snakemake.

samsung-ai-challenge-solution. ⚗️ Samsung AI Challenge for Scientific Discovery 5위 솔루션입니다.

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

snakemake-gatk. :snake::wrench: Snakemake wrappers for GATK.

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

protstruc. Protein structure handling in Python made easy.

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

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

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

learn-sed. :pencil2: SED tutorial

python-mutation-waterfall. :package: Python library for visualizing mutation landscape as waterfall diagram.

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

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"

snakemake-star-rsem-sra. Python

daily-rosalind. :white_check_mark: Solve one rosalind problem per day.

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

snakemake-star-htseq. STAR-HTSeq pipeline in snakemake.

dohlee.github.io. A beautiful, simple, clean, and responsive Jekyll theme for academics

snakemake-bismark-methyldackel-sra. Process SRA bisulfite sequencing data easily with Bismark-MethylDackel pipeline.

meth-pops. Python tool for visualizing methylation status as lollipop diagram.

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

methylome-tools. Tutorials for DNA methylome analysis tools

python-dohlee. :package: My personal python utility library.

snakemake-bwa-strelka2. Python

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

python-cleanlog. :package: Python package for nice colored logs.

viral-lncRNA-cGAS. 💻 Analysis codes and bioinformatics pipelines for paper "Viral long non-coding RNA sequestrates cGAS from HCMV DNA for immune evasion"