bioinformatics
Repositories (1466)
:rocket: seqfu - Sequece Fastx Utilities
CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
💊 AI Research Assistant for Accelerated Drug Discovery. 🦞
BioT5 (EMNLP 2023) and BioT5+ (ACL 2024 Findings)
Generate duplex/single consensus reads to reduce sequencing noises and remove duplications
Explainability techniques for Graph Networks, applied to a synthetic dataset and an organic chemistry task. Code for the workshop paper "Explainabilit...
An NGS read trimming tool that is specific, sensitive, and speedy. (production)
A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
Highly customizable, ambiguity-aware dotplots for visual sequence analyses
Solid Tumor Associative Modeling in Pathology
Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
Single Cell Analysis Pipelines
Get assembly statistics from FASTA and FASTQ files
Mining CRISPRs in Environmental Datasets
:book::books:An introductory tutorial for BioJava
Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
Evaluating genome assemblies
A fast 23andMe DNA parser and inferrer for Python
SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts...
Bio4j abstract model and general entry point to the project
MOLGENIS - for scientific data: management, exploration, integration and analysis.
Physicochemical properties, indices and descriptors for amino-acid sequences.
整理常用的群体遗传学分析流程和脚本
Application of pan-genome for population
Detecting methylation using signal-level features from Nanopore sequencing reads
An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases...
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
MMseqs2 app to run on your workstation or servers
Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells...
Framework for building fast genomics web tools with WebAssembly and WebWorkers
TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
:package: An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/...
(Meta-)genome screening for functional and natural product gene sequences
Fast genomics quality control tools for sequencing data, written in Rust.
tools for reading, writing, generating, merging, and remapping SNPs
A Python package for CD-HIT, clustering protein or nucleotide sequences.
Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab
Demonstrating best practices for bioinformatics command line tools
Dotplot large Genomes in an Interactive, Efficient and Simple way
DEEPScreen: Virtual Screening with Deep Convolutional Neural Networks Using Compound Images
OWLTools
Toolkit for calling structural variants using short or long reads
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
Local version of the virus identification and analysis web server (tool set)
Rapid Profiling and Deconvolution Tool for Metagenomes