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 samtool…

🧬 gget enables efficient querying of genomic reference databases

trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and full-length sequencing datasets.

Hotspot cluster distance analysis in spatial transcriptomic data

Rust Backend for PyRanges Operations. More featureful and much faster replacement for the NCLS library

Blazing-Fast Bioinformatic Operations on Python DataFrames

Evaluate CLIP-seq and other genomic region data using a comprehensive collection of known RBP binding motifs

Python bindings to UCSC BigWig and BigBed library

An open and interoperable data framework for spatial omics data

A lightweight reimplementation of some of the algorithms in the MEME suite in Python.

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

A simple Snakemake profile for Slurm without --cluster-config

A basic template to get started with Snakemake using Pixi

Pydantic-backed validation of delimited text files.

Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.

An awesome tool to visualize snakemake rule graphs