The Top 23 Python Bioinformatics Open Source Projects

Open source projects categorized as Python Bioinformatics

Categories > Data Processing > Bioinformatics

Categories > Programming Languages > Python

Multi Bioner ⭐ 129

Cross-type Biomedical Named Entity Recognition with Deep Multi-task Learning (Bioinformatics'19)

most recent commit 8 months ago

Weblogo ⭐ 128

WebLogo 3: Sequence Logos redrawn

dependent packages 11total releases 15most recent commit 5 months ago

Multiprime ⭐ 123

multiPrime is a mismatch-tolerant minimal primer set design tool for large and diverse sequences (e.g. Virus). Here is a web-based version (test: http://multiPrime.cn))

most recent commit 3 months ago

Oreilly Animal Books For Python ⭐ 123

O‘REILLY animal books for Python

most recent commit 2 years ago

Redundans ⭐ 121

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

most recent commit 4 months ago

Toga ⭐ 120

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

most recent commit 3 months ago

Harmonypy ⭐ 116

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

dependent packages 14total releases 8most recent commit a year ago

Atropos ⭐ 116

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

most recent commit 4 months ago

Cellprofiler Analyst ⭐ 115

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

most recent commit 2 years ago

Ontobio ⭐ 114

python library for working with ontologies and ontology associations

dependent packages 2total releases 190most recent commit 3 months ago

Bio Transformers ⭐ 114

bio-transformers is a wrapper on top of the ESM/Protbert model, trained on millions on proteins and used to predict embeddings.

most recent commit 6 months ago

Kg_rag ⭐ 114

Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks

most recent commit 3 months ago

Lineage ⭐ 114

tools for genetic genealogy and the analysis of consumer DNA test results

total releases 38most recent commit a year ago

Rnalysis ⭐ 114

RNA sequencing analysis software

total releases 43most recent commit 3 months ago

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

dependent packages 3total releases 10most recent commit 3 months ago

Biojava Tutorial ⭐ 111

📖📚An introductory tutorial for BioJava

most recent commit 3 months ago

Pyrodigal ⭐ 111

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

dependent packages 14total releases 60most recent commit 3 months ago

Rapdtool ⭐ 110

Rapid Profiling and Deconvolution Tool for Metagenomes

most recent commit 3 months ago

Mygene.info ⭐ 109

MyGene.info: A BioThings API for gene annotations

most recent commit 3 months ago

Run_dbcan ⭐ 109

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.

total releases 17most recent commit 3 months ago

Squigglekit ⭐ 106

SquiggleKit: A toolkit for manipulating nanopore signal data

most recent commit a year ago

Hamronization ⭐ 105

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure

total releases 4most recent commit 6 months ago

Buddysuite ⭐ 105

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

total releases 18most recent commit 2 years ago

The 10 Most Depended On Python Bioinformatics Open Source Projects

Drep ⭐ 199

Rapid comparison and dereplication of genomes

dependent packages 1total releases 63latest release September 15, 2023most recent commit 7 months ago

Sequence_align ⭐ 39

Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms written in Rust with Python bindings via PyO3.

dependent packages 1total releases 1latest release April 05, 2023most recent commit a year ago

Jpredapi ⭐ 7

Python library and CLI for submitting jobs to JPred - A Protein Secondary Structure Prediction Server

dependent packages 1total releases 7latest release July 20, 2018most recent commit 6 years ago

Bedparse ⭐ 6

Python module and CLI tool to perform operations on BED files

dependent packages 1total releases 7latest release January 23, 2020most recent commit 4 years ago

Pygenomeviz ⭐ 177

A genome visualization python package for comparative genomics

dependent packages 1total releases 23latest release October 28, 2023most recent commit 6 months ago

Parallel Fastq Dump ⭐ 224

parallel fastq-dump wrapper

dependent packages 1total releases 9latest release April 23, 2019most recent commit a year ago

Orange3 Bioinformatics ⭐ 17

🍊🔬 Bioinformatics add-on for Orange3

dependent packages 1total releases 36latest release September 01, 2023most recent commit 3 months ago

Agfusion ⭐ 46

Python package to annotate and visualize gene fusions.

dependent packages 1total releases 38latest release February 10, 2023most recent commit a year ago

Rust_sbml ⭐ 6

SBML parser + bindings to python

dependent packages 1total releases 16latest release November 01, 2021most recent commit a year ago

Molyso ⭐ 6

molyso - Mother Machine Analysis Software

dependent packages 1total releases 7latest release January 12, 2021most recent commit 3 years ago

The 10 Latest Releases In Python Bioinformatics Open Source Projects

Orange3 Bioinformatics ⭐ 17

🍊🔬 Bioinformatics add-on for Orange3

dependent packages 1total releases 36latest release September 01, 2023most recent commit 3 months ago

Pydamage ⭐ 7

Damage parameter estimation for ancient DNA

total releases 14latest release September 01, 2023most recent commit 8 months ago

Decoupler Py ⭐ 112

Python package to perform enrichment analysis from omics data.

dependent packages 3total releases 10latest release August 31, 2023most recent commit 3 months ago

Jcvi ⭐ 650

Python library to facilitate genome assembly, annotation, and comparative genomics

dependent packages 1total releases 97latest release August 30, 2023most recent commit 4 months ago

Janis ⭐ 39

[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows

dependent packages 7total releases 62latest release August 30, 2023most recent commit 8 months ago

Pedl ⭐ 9

Search the biomedical literature for protein interactions and protein associations

total releases 8latest release August 29, 2023most recent commit 5 months ago

Glycowork ⭐ 46

Package for processing and analyzing glycans and their role in biology.

dependent packages 1total releases 9latest release August 27, 2023most recent commit 4 months ago

Instrain ⭐ 104

Bioinformatics program inStrain

total releases 59latest release August 25, 2023most recent commit 8 months ago

Staramr ⭐ 75

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

total releases 18latest release August 24, 2023most recent commit 8 months ago

Plip ⭐ 320

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

dependent packages 1total releases 25latest release August 18, 2023most recent commit 8 months ago

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