SamBryce-Smith
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Python (Bioinformatics)
Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
Pyranges: a Python framework for ultrafast sequence interval operations
Making Snakemake workflows into full-fledged command line tools since 1999.
GFF and GTF file manipulation and interconversion
Efficiently read and write sequencing data from Python
Package for fetching metadata and downloading data from SRA/ENA/GEO
Quality of life improvements for Bioinformatics in Python.
deploy a snakemake pipeline directly from version control (under development)
Incubator for useful bioinformatics code, primarily in Python and R
A high-performance BigWig and BigBed library in Rust
Oxbow makes genomic data ready for high-performance analytics.
This is the development home of the workflow management system Snakemake. For general information, see
A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
Genomic interval operations on Pandas DataFrames
Declarative creation of composable visualization for Python (Complex heatmap, Upset plot, Oncoprint and more~)
Simplifies parallel processing of DNA sequencing reads
Biological sequence analysis for the modern age.
Container class to represent genomic locations and support genomic analysis
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
Feature-rich Python implementation of the tximport package for gene count estimation.
Snakemake workflow management system and CLI generation tool