Python Bioinformatics

Open-source Python projects categorized as Bioinformatics

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
  • InfluxDB

    Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.

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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.

  • 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

  • SaaSHub

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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

  • DnaFeaturesViewer

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

  • biotite

    A comprehensive library for computational molecular biology

  • 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

  • GTDBTk

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

  • sourmash

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

  • bakta

    Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

  • SaaSHub

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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

  • 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
  • Proyectos avanzados de Python?

    1 project | /r/programacion | 19 Jun 2023
  • Need for GUIs for bioinformatic tools?

    3 projects | /r/bioinformatics | 17 Jun 2023
  • A note from our sponsor - InfluxDB
    www.influxdata.com | 30 May 2024
    Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality. Learn more →

Index

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

Project Stars
1 dash 20,653
2 Biopython 4,203
3 deepvariant 3,098
4 scanpy 1,781
5 scispacy 1,622
6 galaxy 1,326
7 deep_gcns_torch 1,118
8 Hail 944
9 ncbi-genome-download 898
10 pyCirclize 642
11 biostar-central 575
12 dash-cytoscape 578
13 DnaFeaturesViewer 561
14 biotite 570
15 PyDESeq2 526
16 dash-bio 516
17 Sniffles 517
18 clinker 505
19 redun 489
20 pyfaidx 442
21 GTDBTk 443
22 sourmash 439
23 bakta 402

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