[<kbd> View page source on GitHub </kbd>](https://github.com/scverse/gget/blob/main/docs/src/en/dependents.md)

# 💡 Active users of this documentation website

[![Heatmap in the form of a world map showing the number of active users of the gget website per country.](https://github.com/lauraluebbert/lauraluebbert/raw/main/gget_user_map.png)](https://github.com/lauraluebbert/lauraluebbert)

Automatically updates every day at 16:00 UTC.

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# ⬇️ Daily `gget` downloads

[![gget PyPI downloads over the last year](https://github.com/lauraluebbert/gget_downloads/raw/main/plots/downloads_gget_daily.png)](https://github.com/lauraluebbert/gget_downloads/tree/main)  
Automatically updates every Sunday at 23:55 UTC.
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# 🧑‍🤝‍🧑 Dependent software
The following applications build on `gget`:
- [gget-mcp](https://mcpindex.net/en/mcpserver/longevity-genie-gget-mcp)
  > "MCP server providing a powerful bioinformatics toolkit for genomics queries and analysis, wrapping the popular **gget** library."
  - Other tools using this or other `gget` MCP servers:
    - [https://mcpservers.org/servers/longevity-genie/holy-bio-mcp](https://mcpservers.org/servers/longevity-genie/holy-bio-mcp)
    - [https://biocontext.ai](https://biocontext.ai/registry/longevity-genie/gget-mcp)
    - [https://mcpmarket.com/zh/tools/skills/gget-bioinformatics-tool](https://mcpmarket.com/zh/tools/skills/gget-bioinformatics-tool)
- [PantheonOS](https://pantheonos.stanford.edu/)  
  An evolvable multi-agent biological agent system designed to reconcile generality with domain specificity being developed at Stanford.  
  > "Database access: using the skills of **gget**, iSeq, and cellxgene to access a variety of databases, including SRA, GEO, Ensembl, UniProt, UCSC, Enrichr, and CZI cellxgene."
- [Biomni](https://biomni.stanford.edu/environment)  
  A General-Purpose Biomedical AI Scientist being developed at Stanford and Genentech.
- [SCIENCECLAW + INFINITE](https://arxiv.org/pdf/2603.14312)  
  A framework for autonomous scientific investigation developed at MIT.  
  > "Tools are grouped into families such as literature [...], genomics (biopython, **gget**), and machine learning (rdkit, pymol)."
- [PerTurboAgent](https://www.biorxiv.org/content/10.1101/2025.05.25.656020v1)  
  A Self-Planning Agent for Boosting Sequential Perturb-seq Experiments.  
  > "We [...] use packages **gget** and blitzgsea for data enrichment analysis"
- [Scientific skills for Claude](https://github.com/K-Dense-AI/claude-scientific-skills) by K-Dense-AI  
  > " This repository contains 138 scientific skills organized across multiple domains. Each skill provides comprehensive documentation, code examples, and best practices for working with scientific libraries, databases, and tools.  
  > 🧬 Bioinformatics & Genomics  
  > Genomic tools: **gget**, ..."
- [Therapeutics Data Commons (TDC)](https://tdcommons.ai/)  
  Artificial intelligence foundation for therapeutic science ([source code](https://github.com/mims-harvard/TDC), [Nat Chem Bio paper](https://www.nature.com/articles/s41589-022-01131-2)) by Harvard's Artificial Intelligence for Medicine and Science lab.
- [BioDiscoveryAgent](https://github.com/snap-stanford/BioDiscoveryAgent)  
  BioDiscoveryAgent is an LLM-based AI agent for closed-loop design of genetic perturbation experiments ([preprint](https://arxiv.org/abs/2405.17631)) by the Stanford Network Analysis Project.
- [DeepChopper](https://ylab-hi.github.io/DeepChopper/)  
  Language models to identify chimeric artificial reads in NanoPore direct-RNA sequencing data by the Yang lab at Northwestern.
- [BRAD](https://github.com/Jpickard1/BRAD)  
  A LLM powered chatbot for bioinformatics ([documentation](https://brad-bioinformatics-retrieval-augmented-data.readthedocs.io/en/latest/index.html), [project main page](https://brad-bioinformatics-retrieval-augmented-data.readthedocs.io/_/downloads/en/latest/pdf/)).
- [scPRINT](https://www.jkobject.com/scPRINT/)  
  scPRINT is a large transformer model built for the inference of gene networks (connections between genes explaining the cell's expression profile) from scRNAseq data ([preprint](https://www.biorxiv.org/content/10.1101/2024.07.29.605556v1)).
- [AnoPrimer](https://sanjaynagi.github.io/AnoPrimer/landing-page.html)  
  AnoPrimer is a Python package for primer design in *An. gambiae* and *An. funestus*, whilst considering genetic variation in wild whole-genome sequenced specimens in malariagen_data.
- [AvaTaR](https://github.com/zou-group/avatar)  
  Optimizing LLM Agents for Tool-Assisted Knowledge Retrieval (NeurIPS 2024) by James Zou Lab at Stanford University.
- [GRLDrugProp](https://github.com/Madscba/GRLDrugProp)  
  Graph representation learning for modelling drug properties.
- [MicrobioLink2](https://github.com/korcsmarosgroup/MicrobioLink2)  
  A computational tool that analyzes the impact of host-microbe interaction on downstream signaling in human cells and tissues.
- Rust implementation of *gget*: [https://github.com/noamteyssier/ggetrs](https://github.com/noamteyssier/ggetrs)
- [https://github.com/Superbio-ai/getbio](https://github.com/Superbio-ai/getbio)
- [https://github.com/yonniejon/AchillesPrediction](https://github.com/yonniejon/AchillesPrediction)
- [https://github.com/ELELAB/cancermuts](https://github.com/ELELAB/cancermuts)
- [https://github.com/Benoitdw/SNPrimer](https://github.com/Benoitdw/SNPrimer)
- [https://github.com/louisjoecodes/a16z-hackathon-project](https://github.com/louisjoecodes/a16z-hackathon-project)
- [https://github.com/EvX57/BACE1-Drug-Discovery](https://github.com/EvX57/BACE1-Drug-Discovery)
- [https://github.com/vecerkovakaterina/hidden-genes-msc](https://github.com/vecerkovakaterina/hidden-genes-msc)
- [https://github.com/vecerkovakaterina/llm_bioinfo_agent](https://github.com/vecerkovakaterina/llm_bioinfo_agent)
- [https://github.com/greedjar74/upstage_AI_Lab](https://github.com/greedjar74/upstage_AI_Lab)
- [https://github.com/alphavector/all](https://github.com/alphavector/all)

See more: [https://github.com/scverse/gget/network/dependents](https://github.com/scverse/gget/network/dependents)

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# 📃 Selected publications using `gget`
- Macrina Lobo et al., [Resolving thyroid lineage cell trajectories merging into a dual endocrine
2 gland in mammals.](https://www.biorxiv.org/content/10.64898/2026.03.11.710917v1.full.pdf) *bioRxiv* (2026). DOI: 10.64898/2026.03.11.710917
  > "Enrichment analysis of differentially expressed genes [...] was performed using **gget enrichr**"
- David Bradley et al., [The fitness cost of spurious phosphorylation.](https://doi.org/10.1038/s44318-024-00200-7) *The EMBO Journal* (2024). DOI: 10.1038/s44318-024-00200-7
  > "Phosphosites matching to putative short linear motifs (SLiMs) were extracted using the **gget elm** resource"
- Mikael Nilsson et al., [Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals.](https://doi.org/10.21203/rs.3.rs-5278325/v1) *Nature Portfolio (under review)* (2024). DOI: 10.21203/rs.3.rs-5278325/v1
  > "Enrichment analysis of differentially expressed genes [...] was performed using **gget enrichr**"
- Avasthi P et al., [Repeat expansions associated with human disease are present in diverse organisms.](https://doi.org/10.57844/arcadia-e367-8b55) *Arcadia* (2024). DOI: 10.57844/arcadia-e367-8b55
  > "We used the gget package using the **gget.blast** command [...] to BLAST our proteins of interest against the non-redundant NCBI protein database"
- Ibrahim Al Rayyes et al., [Single-Cell Transcriptomics Reveals the Molecular Logic Underlying Ca2+ Signaling Diversity in Human and Mouse Brain.](https://doi.org/10.1101/2024.04.26.591400) *bioRxiv* (2024). DOI: 10.1101/2024.04.26.591400
  > "The **gget** package was used to perform the gene set enrichment analyses with databases Reactome_2022 and KEGG_2021_Mouse."
- Beatriz Beamud et al., [Genetic determinants of host tropism in Klebsiella phages.](https://doi.org/10.1016/j.celrep.2023.112048) *Cell Reports* (2023). DOI: 10.1016/j.celrep.2023.112048
  > "Proteins with seemingly enzymatic activity were confirmed to have the characteristic β-helical domain using **gget AlphaFold2**"
- Kimberly Siletti et al., [Transcriptomic diversity of cell types across the adult human brain.](https://doi.org/10.1126/science.add7046) *Science* (2023). DOI: 10.1126/science.add7046
  > "The **gget** package (https://github.com/scverse/gget) was used to perform all gene ontology enrichment analysis"
- David R. Blair & Neil Risch. [Dissecting the Reduced Penetrance of Putative Loss-of-Function Variants in Population-Scale Biobanks.](https://doi.org/10.1101/2024.09.23.24314008) *medRxiv* (2024). DOI: 10.1101/2024.09.23.24314008
  > "Additional gene and transcript information (exon-intron boundaries, 5' and 3' UTRs, full coding and amino acid sequences) was downloaded using **gget**"
- Shanmugampillai Jeyarajaguru Kabilan et al., [Molecular modelling approaches for the identification of potent Sodium-Glucose Cotransporter 2 inhibitors from Boerhavia diffusa for the potential treatment of chronic kidney disease.](https://doi.org/10.21203/rs.3.rs-4520611/v1) *Journal of Computer-Aided Molecular Design (under review)* (2024). DOI: 10.21203/rs.3.rs-4520611/v1
- Joseph M Rich et al., [The impact of package selection and versioning on single-cell RNA-seq analysis.](https://pmc.ncbi.nlm.nih.gov/articles/PMC11014608/#:~:text=10.1101/2024.04.04.588111) *bioRxiv* (2024). DOI: 10.1101/2024.04.04.588111
- Sanjay C. Nagi et al., [AnoPrimer: Primer Design in malaria vectors informed by range-wide genomic variation.](https://wellcomeopenresearch.org/articles/9-255/v1) *Wellcome Open Research* (2024).
- Yasmin Makki Mohialden et al., [A survey of the most recent Python packages for use in biology.](http://dx.doi.org/10.48047/NQ.2023.21.2.NQ23029) *NeuroQuantology* (2023). DOI: 10.48047/NQ.2023.21.2.NQ23029
- Nicola A. Kearns et al., [Generation and molecular characterization of human pluripotent stem cell-derived pharyngeal foregut endoderm.](https://doi.org/10.1016/j.devcel.2023.08.024) *Cell Reports* (2023). DOI: 10.1016/j.devcel.2023.08.024
- Jonathan Rosenski et al., [Predicting gene knockout effects from expression data.](https://link.springer.com/article/10.1186/s12920-023-01446-6) *BMC Medical Genomics* (2023). DOI: 10.1186/s12920-023-01446-6
- Peter Overby et al., [Pharmacological or genetic inhibition of Scn9a protects beta-cells while reducing insulin secretion in type 1 diabetes.](https://doi.org/10.1101/2023.06.11.544521) *bioRxiv* (2023). DOI: 10.1101/2023.06.11.544521
- Mingze Dong et al., [Deep identifiable modeling of single-cell atlases enables zero-shot query of cellular states.](https://doi.org/10.1101/2023.11.11.566161) *bioRxiv* (2023). DOI: 10.1101/2023.11.11.566161

See more: [Google Scholar](https://scholar.google.com/scholar?oi=bibs&hl=en&cites=16153159346512067296,12232900429638659102)
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# 📰 `gget` in the news
- [Oreate AI blog post](https://www.oreateai.com/blog/exploring-alphafold2-a-guide-to-github-repositories-and-colab-resources/e9a4355bf08a6cdfe061cb93d3ff61dd): "Exploring AlphaFold2: A Guide to GitHub Repositories and Colab Resources"
- `gget opentargets` release [blog post](https://blog.opentargets.org/case-study-gget/) by the Open Targets platform
- Documentary short film about *gget*: [https://youtu.be/cVR0k6Mt97o](https://youtu.be/cVR0k6Mt97o)
- Podcast episode for the Prototype Fund Public Interest Podcast about the importance of open-source software and its role in academic research (in German): [https://public-interest-podcast.podigee.io/33-pips4e4](https://public-interest-podcast.podigee.io/33-pips4e4)
- Prototype Fund announcement: [https://prototypefund.de/project/gget-genomische-datenbanken](https://prototypefund.de/project/gget-genomische-datenbanken/)

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# 🚂 [gget code repository](https://github.com/scverse/gget/) traffic
![Plots showing the cumulative clones and views of the gget GitHub repository.](https://raw.githubusercontent.com/scverse/gget/traffic/plots/gget_cumulative_clones_views.png)
Updates automatically every week on Sunday at 23:55 (UTC).
