Packages
ETE3 reconstructs, manipulates, analyzes, and visualizes phylogenetic trees and other tree-like data structures through a Python API.
However, be prepared for high installation friction (likely system dependencies), verify Python version compatibility before installing, and ensure GPLv3 licensing…
scvi-tools provides probabilistic models for analyzing single-cell omics data, including dimensionality reduction, data integration, automated annotation, doublet detection, and spatial deconvolution, built on PyTorch and AnnData.
Install it if you work with single-cell omics data and need probabilistic modeling, integration, or annotation.
Refgenie manages standardized folder structures and indexes for reference genome files, automating organization and retrieval of genomic resources for bioinformatics workflows.
Install it if you work with multiple genomes or need to share genome resources across a team or pipeline.
Varcode loads and analyzes genomic variant data, predicting how DNA variants affect protein sequences by annotating their biological effects on genes and transcripts.
FabIO reads and writes 2D X-ray detector images in 30 different formats from vendors like Mar, Dectris, ADSC, and Hamamatsu, exposing image data as numpy arrays and headers as Python dictionaries.
dnaio reads and writes FASTQ, FASTA, and uBAM files with optimized parsing for bioinformatics workflows, automatically handling compressed formats like .gz, .bz2, .xz, and .zst.
COBRApy is a constraint-based modeling package for genome-scale metabolic network analysis, providing flux balance analysis, flux variability analysis, gene deletion analysis, and access to mathematical solvers.
PyGAD is a Python library for building and running genetic algorithms to optimize single-objective and multi-objective problems, with built-in support for training Keras and PyTorch models.
Install it if you need genetic algorithm optimization; skip it if you only do gradient-based machine learning.
Provides Rust-accelerated triangulation functions for 2D paths and polygons, designed as a backend for napari's spatial geometry operations.
MultiQC scans bioinformatics analysis directories and generates a single interactive HTML report summarizing results across many samples and tools.
Install it if you regularly analyze multiple bioinformatics samples and need unified QC reporting; skip it if you work with single-sample analyses or already have a…
habanero is a low-level Python client for the Crossref search API, enabling programmatic access to bibliographic metadata and publication data from Crossref's database.
Install it if you're building tools that query bibliographic data; skip it only if you need a higher-level abstraction or don't need Crossref's specific data.
Provides a graphical interface for discovering, installing, updating, and uninstalling napari plugins through both pip and conda package managers.
Scikit-multilearn performs multi-label classification tasks using problem-transformation and algorithm-adaptation methods, built on numpy and scikit-learn with a compatible API.
ProLIF generates interaction fingerprints from molecular complexes in MD trajectories, docking simulations, and experimental structures, encoding ligand-protein/DNA/RNA contacts in a machine-readable format.
Provides a Python API to query and retrieve cell metadata and expression data from the CZ CELLxGENE Discover Census, a large-scale single-cell genomics dataset.
Install only if you have network access to the Census service and require Python 3.10 or later.
PyCIFRW reads and writes CIF (Crystallographic Information Format) files, exposing them as nested Python dictionaries for programmatic access to crystallographic data.
Maintenance is aging (last release 508 days ago), so consider it mature rather than actively developed—suitable for production use but not for projects requiring…
Parses GTF (gene transfer format) files into DataFrames, extracting genomic feature annotations with their coordinates, types, and attributes for bioinformatics analysis.