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metheor
☄️ 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
🐍 Snakemake wrappers for bioinformatics.spliceai-pytorch
Implementation of SpliceAI, Illumina's deep neural network to predict variant effects on splicing, in PyTorch.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
🐍🍔 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
🔍 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
🐍🔧 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
✏️ SED tutorialdaily-rosalind
✅ Solve one rosalind problem per day.snakemake-star-rsem-sra
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"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
📦 Python package for nice colored logs.python-mutation-waterfall
📦 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
📦 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
💻 Analysis codes and bioinformatics pipelines for paper "Viral long non-coding RNA sequestrates cGAS from HCMV DNA for immune evasion"samsung-ai-challenge-solution
⚗️ Samsung AI Challenge for Scientific Discovery 5위 솔루션입니다.Love Open Source and this site? Check out how you can help us