Trending repositories for topic bioinformatics
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))
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)
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Feature-rich Python implementation of the tximport package for gene count estimation.
Rapid standardisation and quality control of GWAS or QTL summary statistics
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
Graph-linked unified embedding for single-cell multi-omics data integration
COBRApy is a package for constraint-based modeling of metabolic networks.
Feature-rich Python implementation of the tximport package for gene count estimation.
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))
Rapid standardisation and quality control of GWAS or QTL summary statistics
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)
Graph-linked unified embedding for single-cell multi-omics data integration
COBRApy is a package for constraint-based modeling of metabolic networks.
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Official git repository for Biopython (originally converted from CVS)
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
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 curated list of awesome Bioinformatics libraries and software.
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)
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
Unix, R and python tools for genomics and data science
Python package to perform enrichment analysis from omics data.
ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
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))
Feature-rich Python implementation of the tximport package for gene count estimation.
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
Python package to perform enrichment analysis from omics data.
User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins
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.
Rapid standardisation and quality control of GWAS or QTL summary statistics
A (mostly) universal methylation extractor for BS-seq experiments.
Blender plugin to process biological data and molecular work.
Pegasus Workflow Management System - Automate, recover, and debug scientific computations.
A curated list of awesome Bioinformatics libraries and software.
Official git repository for Biopython (originally converted from CVS)
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.
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
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))
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
Feature-rich Python implementation of the tximport package for gene count estimation.
Unsupervised Deep Disentangled Representation of Single-Cell Omics
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Feature-rich Python implementation of the tximport package for gene count estimation.
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
Unsupervised Deep Disentangled Representation of Single-Cell Omics
A bioinformatics tool written in Rust to find palindromic sequences in DNA
ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery
MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
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.
Awesome-Biomolecule-Language-Cross-Modeling: a curated list of resources for paper "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"
CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.
A Quantum Computing and Machine Learning Model that accelerates the Drug Research and Development process
Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all
A curated list of awesome curated lists of awesome softwares and resources in bioinformatics and affiliated areas
A bioinformatics tool written in Rust to find palindromic sequences in DNA
Fast AlphaFold-Multimer based pipeline for Protein-Protein Interaction (PPI) screening
Feature-rich Python implementation of the tximport package for gene count estimation.
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.
Foldseek enables fast and sensitive comparisons of large structure sets.
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
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))
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Unix, R and python tools for genomics and data science
Multiple Protein Structure Alignment at Scale with FoldMason
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
What should perfect bioinformatic tools be like?
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
This repo is dedicated to make bioinformatics resources available for anyone who wish to enter this field. (You may find it useful or not useful based on your level). I am still embarking my path in t...
FastOMA is a scalable software package to infer orthology relationship.
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.
