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metheor
βοΈ 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)snakemake-wrappers
π 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
π Useful bioinformatics one-line commands.dirichlet-process
Python implementation for nonparametric bayesian clustering with dirichlet process.foldingdiff-pytorch
An unofficial re-implementation of FoldingDiff, a diffusion-based generative model for protein backbone structure generation.snakemake-hamburger
ππ A beginner's guide to modular snakemake workflows.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.prism
π Methylation Pattern-based, Reference-free Inference of Subclonal Makeup. (Lee et al., Bioinformatics. 2019)pysuffixarray
Suffix array implementation written in pythonsnakemake-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.snakemake-star-rsem
STAR-RSEM pipeline in snakemake.snakemake-cartesian-ddg
Snakemake pipeline for Rosetta 'cartesian-ddg' protocol for protein stability prediction upon mutations.rosettafold-pytorch
An unofficial re-implementation of RoseTTAFold, a three-track deep learning model for protein structure prediction.snakemake-gatk
ππ§ Snakemake wrappers for GATK.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.tranception-pytorch
Implementation of Tranception, a SOTA transformer model for protein fitness prediction, in PyTorch.snakemake-star-htseq
STAR-HTSeq pipeline in snakemake.protein-structure-preprocessing
Automated pipeline for preparing protein structure dataset only from a list of PDB ids.learn-sed
βοΈ SED tutorialdaily-rosalind
β Solve one rosalind problem per day.snakemake-star-rsem-sra
dnmt3a-instability-and-methylation-disorder
π» Analysis codes and bioinformatics pipelines for paper "Increased local DNA methylation disorder in AMLs with DNMT3A-destabilizing variants and its clinical implication"protstruc
Protein structure handling in Python made easy.proteinbert-pytorch
Implementation of ProteinBERT, a deep language model designed for proteins.igfold-pytorch
Unofficial re-implementation of IgFold, a fast antibody structure prediction method, in PyTorch.snakemake-bwa-strelka2
deepab-pytorch
An unofficial re-implementation of DeepAb, an interpretable deep learning model for antibody structure prediction.python-cleanlog
π¦ Python package for nice colored logs.python-mutation-waterfall
π¦ Python library for visualizing mutation landscape as waterfall diagram.deeplearning-earlystopping
A minimal python class implementation for early stopping during deep learning model training.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.python-dohlee
π¦ My personal python utility library.eve-pytorch
Implementation of evolutionary model of variant effect (EVE), a deep generative model of evolutionary data, in PyTorch.bpnet-pytorch
Implementation of BPNet, a base-resolution convolutional neural network for transcription-factor binding prediction, in PyTorch.methylome-tools
Tutorials for DNA methylome analysis toolsviral-lncRNA-cGAS
π» Analysis codes and bioinformatics pipelines for paper "Viral long non-coding RNA sequestrates cGAS from HCMV DNA for immune evasion"samsung-ai-challenge-solution
βοΈ Samsung AI Challenge for Scientific Discovery 5μ μ루μ μ λλ€.Love Open Source and this site? Check out how you can help us