#Genomics
Showing 60 of 76 repositories tagged #genomics, ranked by stars
Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 140 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Pi, Antigravity, and the open Agent Skills standard.
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.
Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing.
🧬 gget enables efficient querying of genomic reference databases
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
Python library to facilitate genome assembly, annotation, and comparative genomics
Foundation Models for Genomics & Transcriptomics
Tools to process and analyze deep sequencing data.
Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch
BioMCP: Biomedical Model Context Protocol
Performant Pythonic GenomicRanges
An open source platform for managing and analyzing biomedical big data
Structural variant toolkit for VCFs
A genome visualization python package for comparative genomics
Fast, flexible and extensible genome browser.
Chromosome visualization for the web
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
A genome browser designed for complex structural variants and long reads.
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
Source code for JBrowse 2, a modern React-based genome browser
Tools to work with variant call format files
A list of web-based interactive biological data visualizations.
Ten Quick Tips for Deep Learning in Biology
viral-ngs: command line tools and wrappers for processing raw viral genomic data
MSA(Multiple Sequence Alignment) visualization python package for sequence analysis
Genomic interval operations on Pandas DataFrames
Grammar of Scalable Linked Interactive Nucleotide Graphics
Precision genomics for everyone, everywhere. Powered by private AI.
MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses
Blazing-Fast Bioinformatic Operations on Python DataFrames
A grammar of genomic data transformation
Oxbow makes genomic data ready for high-performance analytics.
A modular annotation tool for genomic variants
Comparative Genomics Toolkit 3
Wally: Visualization of aligned sequencing reads and contigs
Multimodal Data (.h5mu) implementation for Python
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
ClairS - a deep-learning method for long-read somatic small variant calling
Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
Command line utility for manipulating FASTQ files
A tool for drawing ANI clustermap between all-vs-all microbial genomes
Dynamic Kernel Matching (DKM) for Classifying Data with Non-conforming Features
A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
🧬High-performance genetics- and genomics-related data visualization using Makie.jl
ClairS-TO - a deep-learning method for tumor-only somatic variant calling
Genome size estimation from long read overlaps
Provide R access to the NCI Genomic Data Commons portal.
Deep learning for single-cell transcript counts
Rapid population clustering with autoencoders
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
OhmNet: Representation learning in multi-layer graphs
A tool for classifying prokaryote protein sequences into COG(Cluster of Orthologous Genes) functional category
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
Model and predict short DNA sequence features with neural networks
A small project to add ggplot2 extensions
Merging, Annotation, Validation, and Illustration of Structural variants
convert various features into a GFF-like file for use in genome browsers
This repository gives an overview of my teaching activities. Links to slides and data sets are included. Feel free to re-use my content.
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.