Pyrodigal
Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes - Published in JOSS (2022)
rdflib
RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
pyCeterisParibus
pyCeterisParibus: explaining Machine Learning models with Ceteris Paribus Profiles in Python - Published in JOSS (2019)
spatial-efd
spatial-efd: A spatial-aware implementation of elliptical Fourier analysis - Published in JOSS (2017)
mmappickle
mmappickle: Python 3 module to store memory-mapped numpy array in pickle format - Published in JOSS (2018)
georasters
GeoRasters is a Python module that provides a fast and flexible tool to work with GIS raster files.
pyskani
PyO3 bindings and Python interface to skani, a method for fast genomic identity calculation using sparse chaining.
pyfastani
Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
dedupe
:id: A python library for accurate and scalable fuzzy matching, record deduplication and entity-resolution.
https://github.com/alan-turing-institute/clevercsv
CleverCSV is a Python package for handling messy CSV files. It provides a drop-in replacement for the builtin CSV module with improved dialect detection, and comes with a handy command line application for working with CSV files.
https://github.com/pypr/pysph
A framework for Smoothed Particle Hydrodynamics in Python
acttensor-tf
ActTensor: Activation Functions for TensorFlow. https://pypi.org/project/ActTensor-tf/ Authors: Pouya Ardehkhani, Pegah Ardehkhani
rich
Rich is a Python library for rich text and beautiful formatting in the terminal.
pyglotaran
A Python library for Global and Target Analysis of time-resolved spectroscopy data
pymunk
Pymunk is a easy-to-use pythonic 2d physics library that can be used whenever you need 2d rigid body physics from Python
https://github.com/althonos/pyopal
Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.
gitpython
GitPython is a python library used to interact with Git repositories.
cbsodata
Unofficial Statistics Netherlands (CBS) open data API client for Python
augur
Python library and web service for Open Source Software Health and Sustainability metrics & data collection. You can find our documentation and new contributor information easily here: https://oss-augur.readthedocs.io/en/main/
wikes-toolkit
a user-friendly toolkit for the Wiki-Entity-Summarization (WikES) project.
https://github.com/althonos/pyfamsa
Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.
https://github.com/althonos/pyjess
Cython bindings and Python interface to Jess, a 3D template matching software for protein structures.
https://github.com/datamade/usaddress
:us: a python library for parsing unstructured United States address strings into address components
https://github.com/althonos/mini3di
A NumPy port of the foldseek code for encoding protein structures to 3di.
https://github.com/althonos/pyaragorn
Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.
https://github.com/althonos/pytantan
Cython bindings and Python interface to Tantan, a fast method for identifying repeats in DNA and protein sequences.
https://github.com/althonos/diced
A Rust reimplementation of the MinCED method for identifying CRISPRs in full or assembled genomes.
distro
A much more elaborate replacement for removed Python's `platform.linux_distribution()` method
icclim
icclim: Python library for climate indices and climate indicators calculation.
https://github.com/althonos/torch-treecrf
A PyTorch implementation of Tree-structured Conditional Random Fields.
https://github.com/althonos/pytrimal
Cython bindings and Python interface to trimAl, a tool for automated alignment trimming. Now with SIMD!
https://github.com/broadinstitute/funpipe
A python3 library for building best practice fungal genomic analysis pipeline
upgini
Data search & enrichment library for Machine Learning → Easily find and add relevant features to your ML & AI pipeline from hundreds of public and premium external data sources, including open & commercial LLMs
https://github.com/akamhy/imagedominantcolor
Get the dominant color of any image
https://github.com/habedi/feature-factory
A feature engineering library for Rust 🦀 with Python bindings 🐍
gema
A small Python 3 library to train Self Organizing Maps and use them to classify patterns.
https://github.com/prolint/prolint2
Prolint2 is an optimized tool for analyzing and visualizing lipid-protein interactions from molecular dynamics trajectories.
sentinelhub-py
Download and process satellite imagery in Python using Sentinel Hub services.
https://github.com/ayaanhossain/sharedb
An on-disk pythonic embedded key-value store for compressed data storage and distributed data analysis
bcl
Python library that provides a simple interface for symmetric (i.e., secret-key) and asymmetric (i.e., public-key) encryption/decryption primitives.
https://github.com/althonos/property-cached
A (better) decorator for caching properties in classes (forked from cached-property).
crosspm
Universal Cross Package Manager - allows you to use the manifest file to download packages of various formats from different storage locations.
https://github.com/althonos/rlinalg
Linear Algebra routines for Python as implemented in the R language.
pi-ina219
This Python library supports the INA219 voltage, current and power monitor from Texas Instruments with a Raspberry Pi using the I2C bus. The intent of the library is to make it easy to use the quite complex functionality of this sensor.
https://github.com/althonos/pymuscle5
Cython bindings and Python interface to MUSCLE v5, a highly efficient and accurate multiple sequence alignment software.
https://github.com/althonos/nanoset.py
A memory-optimized wrapper for Python sets likely to be empty.
manorm2-utils
To pre-process a set of ChIP-seq samples and coordinate with MAnorm2 for differential analysis
https://github.com/devparihar5/outlyzer
Outlyzer is a Python library for outlier detection that offers various methods for identifying and visualizing outliers in datasets.
https://github.com/erictleung/lalg
:recycle: Python library to experiment with Linear Algebra concepts (work in progress)
https://github.com/nsembleai/nsvision
nsvision is the image data pre and post processing and data augmentation library. It provides utilities for working with image data.
ontoaligner
OntoAligner: A Python Toolkit for Ontology Alignment https://pypi.org/project/OntoAligner/
hinteval
HintEval💡: A Comprehensive Framework for Hint Generation and Evaluation for Questions
https://github.com/ampliconsuite/ampliconclassifier
Classify output of AmpliconArchitect to detect types of focal amplifications present
ontolearner
OntoLearner: A Modular Python Library for Ontology Learning with LLMs https://pypi.org/project/OntoLearner/
https://github.com/althonos/pyncbitk
Cython bindings and Python interface to the NCBI C++ ToolKit (including BLAST+).
https://github.com/cea-metrocarac/pysspfm
PySSPFM: A specialized tool for Switching Spectroscopy Piezoresponse Force Microscopy (SSPFM) data processing
pycoupler
An LPJmL-Python interface for operating LPJmL in a Python environment and coupling it with Python models, programmes or simple programming scripts.
architxt
ArchiTXT is an open source Python library that transforms unstructured text into structured, searchable, and AI-ready data. It enables automated database generation and seamless data integration.
https://github.com/omigutin/img_ops
Is a minimal, device‑aware image ops library built on top of OpenCV and NumPy.
