Python Bioinformatics

Open-source Python projects categorized as Bioinformatics
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Topics: Python Genomics Data Science Machine Learning Deep Learning
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Top 23 Python Bioinformatic Projects

  • dash

    Data Apps & Dashboards for Python. No JavaScript Required.

    • Project mention: dash VS solara - a user suggested alternative | libhunt.com/r/dash | 2023-10-13

  • Biopython

    Official git repository for Biopython (originally converted from CVS)

    • Project mention: Invitación a proyecto - Biopython en Español | /r/devsarg | 2023-07-23

  • WorkOS

    The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.

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  • deepvariant

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

    • Project mention: Look over my purchase, is there anything I should return? | /r/buildapc | 2023-05-06

  • scanpy

    Single-cell analysis in Python. Scales to >1M cells.

    • Project mention: Renaming Genes for Scanpy Plot | /r/bioinformatics | 2023-06-15

  • scispacy

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

  • galaxy

    Data intensive science for everyone.

    • Project mention: Need for GUIs for bioinformatic tools? | /r/bioinformatics | 2023-06-17

    Maybe it would help you to look at the galaxy project: GitHub main site

  • deep_gcns_torch

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

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  • Hail

    Cloud-native genomic dataframes and batch computing

  • ncbi-genome-download

    Scripts to download genomes from the NCBI FTP servers

  • pyCirclize

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

  • biostar-central

    Biostar Q&A

    • Project mention: Forums/Communites for Bioinformatics on Other Platforms? | /r/bioinformatics | 2023-06-22

    Biostars is a great community, basically a bioinformatics-focused version of stackoverflow.

  • dash-cytoscape

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

  • biotite

    A comprehensive library for computational molecular biology

  • DnaFeaturesViewer

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

  • PyDESeq2

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

    • Project mention: DESeq2 Normalization | /r/bioinformatics | 2023-06-09

    https://github.com/owkin/PyDESeq2/blob/main/pydeseq2/preprocessing.py I'm not sure but only a normalized count matrix seems not enough to do differential expression analysis. For example, in this script, it gathers also the size factor from the raw read count matrix. Maybe you could find it somewhere or recalculate it.

  • dash-bio

    Open-source bioinformatics components for Dash

    • Project mention: Bam viewer with custom fasta reference that's embeddable in Streamlit app? | /r/bioinformatics | 2023-06-30

    dash-bio This is another great choice, but unlike standard plotly figures, I need to find how to embedd dash widgets into streamlit. It seems possible, but it's not clear how to do it.

  • Sniffles

    Structural variation caller using third generation sequencing

  • clinker

    Gene cluster comparison figure generator

  • redun

    Yet another redundant workflow engine

    • Project mention: Redun: Yet another redundant workflow engine | news.ycombinator.com | 2023-08-11

  • pyfaidx

    Efficient pythonic random access to fasta subsequences

  • sourmash

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

  • GTDBTk

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

  • bakta

    Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  • SaaSHub

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

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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 Bioinformatics related posts

Index

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

Project Stars
1 dash 20,472
2 Biopython 4,158
3 deepvariant 3,076
4 scanpy 1,745
5 scispacy 1,612
6 galaxy 1,313
7 deep_gcns_torch 1,104
8 Hail 934
9 ncbi-genome-download 887
10 pyCirclize 604
11 biostar-central 573
12 dash-cytoscape 571
13 biotite 554
14 DnaFeaturesViewer 545
15 PyDESeq2 510
16 dash-bio 510
17 Sniffles 505
18 clinker 501
19 redun 484
20 pyfaidx 440
21 sourmash 432
22 GTDBTk 426
23 bakta 389

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