Python computational-biology

Open-source Python projects categorized as computational-biology
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Top 8 Python computational-biology Projects

  • OpenChem

    OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

    • Project mention: Computational Chemistry Using PyTorch | news.ycombinator.com | 2023-07-22

  • dash-cytoscape

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

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  • biotite

    A comprehensive library for computational molecular biology

  • dance

    DANCE: a deep learning library and benchmark platform for single-cell analysis (by OmicsML)

  • Clairvoyante

    Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

  • metaGEM

    :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

    • Project mention: Metagenomic samples analysis: From taxonomic classification to reads mapping | /r/bioinformatics | 2023-06-09

    Maybe this workflow will be interesting to you: it assembles metagenomes, generates bins, and also creates metabolic models for predicting interactions within microbiomes 💎 https://github.com/franciscozorrilla/metaGEM

  • PteraSoftware

    Ptera Software is a fast, easy-to-use, and open-source software package for analyzing flapping-wing flight.

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  • CNApy

    An integrated visual environment for metabolic modeling with common methods such as FBA, FVA and Elementary Flux Modes, and advanced features such as thermodynamic methods, extended Minimal Cut Sets, OptKnock, RobustKnock, OptCouple and more!

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).

Python computational-biology related posts

  • Metagenomic samples analysis: From taxonomic classification to reads mapping

    1 project | /r/bioinformatics | 9 Jun 2023

  • Is Developing a Multi-omics Pipeline Feasable for a Masters Thesis?

    1 project | /r/bioinformatics | 19 May 2023

  • Favorite Pipeline/Methods Figure

    4 projects | /r/bioinformatics | 24 Feb 2023

  • Why bother reconstructing MAGs ?

    2 projects | /r/bioinformatics | 11 Jan 2023

  • MetaQuast for assembling samples from complex communities

    1 project | /r/bioinformatics | 27 Jul 2022

  • Finding BGCs from antiSMASH database in metagenomes

    1 project | /r/bioinformatics | 21 Jul 2022

  • Need guidance/plan/roadmap to transition from bioinformatics to systems biology and netwrok biology.

    1 project | /r/bioinformatics | 15 Jul 2022
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    www.saashub.com | 10 May 2024
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Index

What are some of the best open-source computational-biology projects in Python? This list will help you:

Project Stars
1 OpenChem 657
2 dash-cytoscape 573
3 biotite 560
4 dance 323
5 Clairvoyante 172
6 metaGEM 168
7 PteraSoftware 155
8 CNApy 41

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