Trending repositories for topic bioinformatics
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)
Versatile computational pipeline for processing protein structure data for deep learning applications.
A curated list of awesome Bioinformatics libraries and software.
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
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 python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Multiple Protein Structure Alignment at Scale with FoldMason
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Versatile computational pipeline for processing protein structure data for deep learning applications.
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
Multiple Protein Structure Alignment at Scale with FoldMason
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only 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))
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Scientific Computing for Chemists text for teaching basic computing skills to chemistry students using Python, Jupyter notebooks, and the SciPy stack. This text makes use of a variety of packages incl...
:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)
DANCE: a deep learning library and benchmark platform for single-cell analysis
Versatile computational pipeline for processing protein structure data for deep learning applications.
Official git repository for Biopython (originally converted from CVS)
A curated list of awesome Bioinformatics libraries and software.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only 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))
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Multiple Protein Structure Alignment at Scale with FoldMason
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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.
Versatile computational pipeline for processing protein structure data for deep learning applications.
Exon is an OLAP query engine specifically for biology and life science applications.
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Multiple Protein Structure Alignment at Scale with FoldMason
Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.
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 python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
Multiple Protein Structure Alignment at Scale with FoldMason
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.
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
Versatile computational pipeline for processing protein structure data for deep learning applications.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Foldseek enables fast and sensitive comparisons of large structure sets.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
An open-source pathogen sequence database dedicated to equitable sharing, transparent governance, & empowering global public health.
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only 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))
Multiple Protein Structure Alignment at Scale with FoldMason
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
Exon is an OLAP query engine specifically for biology and life science applications.
Versatile computational pipeline for processing protein structure data for deep learning applications.
Fast and space-efficient taxonomic classification of long reads
Python package to obtain, parse and explore biological taxonomies (GTDB, NCBI, Silva, Greengenes, OTT)
Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic 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))
Ultimate ATAC-seq Data Processing & Quantification Workflow. A Snakemake implementation of the BSF's ATAC-seq Data Processing Pipeline extended by downstream quantification and annotation steps using ...
kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
Awesome-Biomolecule-Language-Cross-Modeling: a curated list of resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"
DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
A Quantum Computing and Machine Learning Model that accelerates the Drug Research and Development process
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
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...
kmer based feature extraction tool for bioinformatics, metagenomics, AI/ML and more
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.
Foldseek enables fast and sensitive comparisons of large structure sets.
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
MMseqs2: ultra fast and sensitive search and clustering suite
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
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))
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
A full spaCy pipeline and models for scientific/biomedical documents.
Cell2Sentence turns scRNA-seq data into text for LLM training.
What should perfect bioinformatic tools be like?
Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Simple phylogenetic tree visualization python package for phylogenetic analysis
🌿: ABM & GIS for philological, archaeological, and anthropological 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))
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Exon is an OLAP query engine specifically for biology and life science applications.
Detection of remote homology by comparison of protein language model representations