Open-source alternatives to Bioservices

Efficient pythonic random access to fasta subsequences

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

Scanpy is a Python library for the preprocessing, visualization, and analysis of large-scale single-cell gene expression datasets. It serves as a toolkit for single-cell RNA sequencing analysis, providing a framework to process and analyze genomic data from individual cells to identify biological markers and cell types. The library includes a scalable data processing pipeline for cleaning and preparing genomic data, a clustering framework for grouping cells with similar expression profiles, and a system for modeling transitions between cell states to reconstruct biological development and dif