Biological Data Analysis Python Packages

protpy

Calculating a range of protein descriptors using their physicochemical, biological and structural properties 🔬.

py3plex

Py3plex - A multilayer complex network visualization and analysis library in python3

openflo

Openflo: a open source flow cytometry repo with flowjo compatibility and automation pipeline

squarna

RNA secondary structure prediction tool

phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

aop2db

Convert the AOP Wiki database to a relational database.

mnnpy

An implementation of MNN (Mutual Nearest Neighbors) correct in python.

lam

LAM is a quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images.

fuse-toolkit

FUSE toolkit supports fluorescent cell image alignment and analysis.

deepcell-spots

Deep Learning Library for Spot Detection

devolearn

Accelerate data driven research on embryos with deep learning models :microscope:

bioviper

Enhancements to Biopython for working with biological data

pylattice

A python library for advanced lattice light-sheet image analysis

memocell

Bayesian inference of stochastic cellular processes with and without memory in Python.

plugy

Flexible processing and analysis of plug microfluidics data

metrics-petri

Python package repository for quantifying Magnaporthe oryzae colony growth, morphology, cracking, and texture from time-series Petri-dish images.

artem-rna

RNA/DNA 3D structure alignment tool

med-signal

A python package designed to simulate and analize EEG signals to determine relevant data and study cases.

pycellid

Functions to analyze Cell-ID single-cell cytometry data using python language.

pepnet

Neural networks for amino acid sequences

medsig

A python package designed to simulate and analize EEG signals to determine relevant data and study cases.