Repository Index

Data Apps & Dashboards for Python. No JavaScript Required.

• dash
• plotly
• data-visualization
• data-science

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library

A dependency-free cross-platform swiss army knife for PDB files.

• python
• protein
• pdb
• bioinformatics

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

Autonomous multi-agent framework to optimize scientific software

• acceleration
• agentic-ai
• ai-agents
• bioinformatics

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution

UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.

• benchmark
• bioinformatics
• cheminformatics
• computational-chemistry

Bioinformatics-themed kata for practicing string manipulation in a data transformation pipeline. Contains replit files to work quickly in an online dojo setting.

• kata
• challenge
• python
• bioinformatics