Trending repositories for topic bioinformatics
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Official git repository for Biopython (originally converted from CVS)
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
A curated list of Cheminformatics libraries and software.
A comprehensive library for computational molecular biology
Unix, R and python tools for genomics and data science
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
A fully reproducible and state-of-the-art ancient DNA analysis pipeline
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
A curated list of Cheminformatics libraries and software.
A comprehensive library for computational molecular biology
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Unix, R and python tools for genomics and data science
Official git repository for Biopython (originally converted from CVS)
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Official git repository for Biopython (originally converted from CVS)
A curated list of awesome Bioinformatics libraries and software.
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
quickly filter fastq files by matching sequences to a set of regex patterns
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
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.
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
quickly filter fastq files by matching sequences to a set of regex patterns
ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
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
Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Inference of ploidy and heterozygosity structure using whole genome sequencing data
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
A simple Snakemake profile for Slurm without --cluster-config
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
A curated list of awesome Bioinformatics libraries and software.
Official git repository for Biopython (originally converted from CVS)
quickly filter fastq files by matching sequences to a set of regex patterns
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
A comprehensive library for computational molecular biology
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.
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
quickly filter fastq files by matching sequences to a set of regex patterns
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
FastOMA is a scalable software package to infer orthology relationship.
Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in genomes.
ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
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.
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NIH
NeuroGNN is a state-of-the-art framework for precise seizure detection and classification from EEG data. It employs dynamic Graph Neural Networks (GNNs) to capture intricate spatial, temporal, semanti...
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.
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!
A curated list of awesome curated lists of awesome softwares and resources in bioinformatics and affiliated areas
ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
A bioinformatics tool written in Rust to find palindromic sequences in DNA
Feature-rich Python implementation of the tximport package for gene count estimation.
Fast AlphaFold-Multimer based pipeline for Protein-Protein Interaction (PPI) screening
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
Official git repository for Biopython (originally converted from CVS)
A curated list of awesome Bioinformatics libraries and software.
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
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.
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))
Unix, R and python tools for genomics and data science
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Multiple Protein Structure Alignment at Scale with FoldMason
What should perfect bioinformatic tools be like?
Affinity Protein-Protein Transformers—State of the art protein-protein binding affinity in seconds!
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
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/
