Popular GitHub Repositories for Bioinformatics

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

A full spaCy pipeline and models for scientific/biomedical documents.

Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

Python package for graph neural networks in chemistry and biology

Precision Medicine Knowledge Graph (PrimeKG)

一种基于迭代多大型语言模型的共识框架，用于提高单细胞RNA测序数据中细胞类型注释的准确性

? A curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)

DANCE: a deep learning library and benchmark platform for single-cell analysis

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

? immunarch [R package] – Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

Single cell perturbation prediction

ECG classification programs based on ML/DL methods

BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

Ten Quick Tips for Deep Learning in Biology

Awesome-Biomolecule-Language-Cross-Modeling: a curated list of resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"

Plant Disease Identification Using Convulutional Neural Network

BioGrakn Knowledge Graph

SGAS: Sequential Greedy Architecture Search (CVPR'2020) https://www.deepgcns.org/auto/sgas