Trending repositories for topic bioinformatics
A curated list of awesome Bioinformatics libraries and software.
Foldseek enables fast and sensitive comparisons of large structure sets.
Blazing-Fast Bioinformatic Operations on Python DataFrames
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
quickly filter fastq files by matching sequences to a set of regex patterns
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Interactive network visualization in Python and Dash, powered by Cytoscape.js
Unix, R and python tools for genomics and data science
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
Blazing-Fast Bioinformatic Operations on Python DataFrames
quickly filter fastq files by matching sequences to a set of regex patterns
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Scikit-learn compatible library for molecular fingerprints
A tool for cell instance aware segmentation in densely packed 3D volumetric images
What should perfect bioinformatic tools be like?
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
Foldseek enables fast and sensitive comparisons of large structure sets.
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Interactive network visualization in Python and Dash, powered by Cytoscape.js
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
A curated list of awesome Bioinformatics libraries and software.
Blazing-Fast Bioinformatic Operations on Python DataFrames
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Unix, R and python tools for genomics and data science
Scikit-learn compatible library for molecular fingerprints
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Official git repository for Biopython (originally converted from CVS)
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
Blazing-Fast Bioinformatic Operations on Python DataFrames
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
quickly filter fastq files by matching sequences to a set of regex patterns
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
protein structure generation with sparse all-atom denoising models
Scikit-learn compatible library for molecular fingerprints
What should perfect bioinformatic tools be like?
Fast and accurate label-free quantification for small and very large numbers of proteomes
A community-focused repository dedicated to fostering learning and development in Artificial Intelligence 🚀. This project, created by me, @Genetifics, aims to provide high-quality, accessible, and fr...
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
A curated list of awesome Bioinformatics libraries and software.
Official git repository for Biopython (originally converted from CVS)
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
Foldseek enables fast and sensitive comparisons of large structure sets.
Blazing-Fast Bioinformatic Operations on Python DataFrames
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
Scikit-learn compatible library for molecular fingerprints
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
A comprehensive library for computational molecular biology
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Unix, R and python tools for genomics and data science
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
Blazing-Fast Bioinformatic Operations on Python DataFrames
protein structure generation with sparse all-atom denoising models
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Rust crates for working with Workflow Description Language (WDL) documents.
A Rust-based, headless workflow execution framework supporting local, cloud, and HPC.
Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in genomes.
quickly filter fastq files by matching sequences to a set of regex patterns
Searching for structural similarities across billions of molecules in milliseconds
Scikit-learn compatible library for molecular fingerprints
A comparative genomics workflow using Nextflow, conda, Julia and R
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
I am sharing my code repository to understand the working and principle of working of various BioInformatics code in Python
CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
[ICLR'25] ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
A curated list of awesome curated lists of awesome softwares and resources in bioinformatics and affiliated areas
Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in genomes.
Fast AlphaFold-Multimer based pipeline for Protein-Protein Interaction (PPI) screening
Feature-rich Python implementation of the tximport package for gene count estimation.
A Rust-based, headless workflow execution framework supporting local, cloud, and HPC.
A bioinformatics tool written in Rust to find palindromic sequences in DNA
A curated list of awesome Bioinformatics libraries and software.
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Official git repository for Biopython (originally converted from CVS)
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Foldseek enables fast and sensitive comparisons of large structure sets.
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn)
A comprehensive library for computational molecular biology
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Unix, R and python tools for genomics and data science
Multiple Protein Structure Alignment at Scale with FoldMason
MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses
Scikit-learn compatible library for molecular fingerprints
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
protein structure generation with sparse all-atom denoising models
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
A deep learning model (EVO2-500M) for predicting host specificity of eukaryote-infecting viruses CDNA sequence
A Rust-based, headless workflow execution framework supporting local, cloud, and HPC.
Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
FastOMA is a scalable software package to infer orthology relationship.
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/