Top 23 Python Bioinformatic Projects

Bioinformatics

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1. dash

   1 56 22,194 9.2 Python

   Data Apps & Dashboards for Python. No JavaScript Required.

   

2. CodeRabbit

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3. Biopython

   2 32 4,535 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.

4. deepvariant

   3 5 3,346 9.4 Python

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

   

5. scanpy

   4 5 2,045 9.2 Python

   Single-cell analysis in Python. Scales to >100M cells.

   

6. scispacy

   5 2 1,779 5.7 Python

   A full spaCy pipeline and models for scientific/biomedical documents.

   

7. galaxy

   6 4 1,473 10.0 Python

   Data intensive science for everyone.

   

8. deep_gcns_torch

   7 1 1,145 0.0 Python

   Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org

   

9. SaaSHub

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10. Hail

    8 6 998 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

11. ncbi-genome-download

    9 4 988 5.2 Python

    Scripts to download genomes from the NCBI FTP servers

    

12. scikit-bio

    10 2 919 8.8 Python

    scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

    

13. pyCirclize

    11 7 845 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

14. biotite

    12 2 762 9.6 Python

    A comprehensive library for computational molecular biology

    

15. PyDESeq2

    13 2 633 8.5 Python

    A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.

    

16. dash-cytoscape

    14 1 627 5.8 Python

    Interactive network visualization in Python and Dash, powered by Cytoscape.js

    

17. DnaFeaturesViewer

    15 2 619 0.0 Python

    :eye: Python library to plot DNA sequence features (e.g. from Genbank files)

    

18. biostar-central

    16 10 585 0.9 Python

    Biostar Q&A

    

19. Sniffles

    17 1 583 8.7 Python

    Structural variation caller using third generation sequencing

    

20. clinker

    18 2 557 5.4 Python

    Gene cluster comparison figure generator

    

21. redun

    19 4 542 7.6 Python

    Yet another redundant workflow engine

    

22. dash-bio

    20 2 541 4.7 Python

    Open-source bioinformatics components for Dash

    

23. GTDBTk

    21 1 505 5.4 Python

    GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

    

24. sourmash

    22 1 491 9.5 Python

    Quickly search, compare, and analyze genomic and metagenomic data sets.

    

25. bakta

    23 1 490 8.9 Python

    Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

    

26. SaaSHub

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    SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

    

Python Bioinformatics related posts

• Workflow Engine for In-Silico Biology

  2 projects | news.ycombinator.com | 27 Jul 2024

• Circular Data Visualization in Python

  1 project | news.ycombinator.com | 9 Jul 2024

• R pipelines for bulk RNA-seq analyses

  3 projects | /r/bioinformatics | 9 Dec 2023

• Nextflow: Data-Driven Computational Pipelines

  9 projects | news.ycombinator.com | 10 Aug 2023

• Invitación a proyecto - Biopython en Español

  1 project | /r/devsarg | 23 Jul 2023

• Bam viewer with custom fasta reference that's embeddable in Streamlit app?

  6 projects | /r/bioinformatics | 30 Jun 2023

• Forums/Communites for Bioinformatics on Other Platforms?

  1 project | /r/bioinformatics | 22 Jun 2023
• A note from our sponsor - CodeRabbit
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