Top 23 Python Genomic Projects

Genomics

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1. Biopython

   1 32 4,524 9.4 Python

   Official git repository for Biopython (originally converted from CVS)

   

   Project mention: How to Start Contributing to Open Source Software | dev.to | 2024-10-17

   I also like contributing specifically to my field. As a PhD student and possibly future scientist, I have a vested interest in the quality of the software in my field–specifically, structural bioinformatics. I use several tools in this field and often find areas that can be improved, both for myself and others. As an example, consider this minor documentation change I added to the Biopython documentation.

2. CodeRabbit

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3. deepvariant

   2 5 3,341 9.4 Python

   DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

   

4. galaxy

   3 4 1,464 10.0 Python

   Data intensive science for everyone.

   

5. Hail

   4 6 997 9.4 Python

   Cloud-native genomic dataframes and batch computing

   

   Project mention: Ask HN: Who is hiring? (October 2024) | news.ycombinator.com | 2024-10-01

6. ncbi-genome-download

   5 4 988 5.2 Python

   Scripts to download genomes from the NCBI FTP servers

   

7. pyCirclize

   6 7 833 8.4 Python

   Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

   

   Project mention: Circular Data Visualization in Python | news.ycombinator.com | 2024-07-09

8. goatools

   7 2 808 5.7 Python

   Python library to handle Gene Ontology (GO) terms

   

9. SaaSHub

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10. eggnog-mapper

    8 1 596 3.8 Python

    Fast genome-wide functional annotation through orthology assignment

    

11. nucleotide-transformer

    9 2 579 5.3 Python

    🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

    

    Project mention: Nucleotide Transformer: building robust foundation models for human genomics | news.ycombinator.com | 2024-12-07

    Any given segment of DNA within a gene can classified as ignored, transcribed into RNA and spliced into another segment, can signal to start or end a splice, can signal the start or end of the protein, can be a regulatory switch for other parts of DNA, and more...

    This LLM takes a DNA sequence and assigns probabilities for each of those classifications: https://github.com/instadeepai/nucleotide-transformer .

12. enformer-pytorch

    10 1 465 4.5 Python

    Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

    

13. pyfaidx

    11 1 466 6.2 Python

    Efficient pythonic random access to fasta subsequences

    

14. DNA-Diffusion

    12 4 382 3.9 Python

    🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

    

15. truvari

    13 1 344 9.4 Python

    Structural variant toolkit for VCFs

    

16. pyGenomeViz

    14 3 312 8.7 Python

    A genome visualization python package for comparative genomics

    

17. hgvs

    15 1 260 7.2 Python

    Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

    

18. Scoary

    16 2 190 0.0 Python

    Pan-genome wide association studies

    

19. ariba

    17 1 172 3.0 Python

    Antimicrobial Resistance Identification By Assembly

    

20. veba

    18 3 83 8.2 Python

    A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

    

21. ClipKIT

    19 1 70 5.1 Python

    a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

    

22. covid-19-genomes

    20 1 52 8.7 Python

    Projects on COVID-19 topic of genomic sequencing - mostly DataViz

    

23. UPIMAPI

    21 3 31 4.9 Python

    UniProt Id Mapping through API

    

24. arcsv

    22 1 28 3.5 Python

    Complex structural variant detection from WGS data

    

25. enrich_omics

    23 2 19 2.8 Python

    A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

    

26. SaaSHub

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Python Genomics related posts

• Invitación a proyecto - Biopython en Español

  1 project | /r/devsarg | 23 Jul 2023

• Snakemake – A framework for reproducible data analysis

  6 projects | news.ycombinator.com | 15 Jul 2023

• Biopython – Python Tools for Computational Molecular Biology

  1 project | news.ycombinator.com | 28 May 2023

• comparing the similarity between a set of protein sequences

  2 projects | /r/genomics | 12 May 2023

• Look over my purchase, is there anything I should return?

  2 projects | /r/buildapc | 6 May 2023

• u/Responsible-Gas3852 comments on "Why is Cancer so Hard to Cure?"

  2 projects | /r/bestof | 13 Apr 2023

• My boss is considering letting me take a programming course if I have some good reasons why.

  2 projects | /r/labrats | 13 Apr 2023
• A note from our sponsor - SaaSHub
  www.saashub.com | 18 Mar 2025

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