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Cython bindings and Python interface to Jess, a 3D template matching software.

Cython bindings and Python interface to FAMSA, an algorithm for ultra-scale multiple sequence alignments.

A NumPy port of the NEAR code for embedding protein sequences.

A NumPy port of the foldseek code for encoding protein structures to 3di.

PyO3 bindings and Python interface to skani, a method for fast fast genomic identity calculation using sparse chaining.

Cython bindings and Python interface to trimAl, a tool for automated alignment trimming.

Shiny app designed by Ben Johnson to quickly analyze calcium trace outputs. Attached manual to explain the parameters and how to analyze your traces.

Cython bindings and Python interface to ARAGORN, a (t|mt|tm)RNA gene finder.

A lightweight platform-accelerated library for biological motif scanning using position weight matrices.

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes.

Cython bindings and Python interface to HMMER3.

Repository containing a Snakemake ChIPseq pipeline for SE and PE datasets

Repository for Jianhui's snakemake pipeline

This repository gather all genomics data and analysis we performed on Zbtb24 in mouse embryonic stem cells.

Dependency free, Cython-compatible scoring matrices to use with biological sequences.

Gene Clusters with Conditional Random Fields.

This is meant as a playground for learning some basics in version control and code collaboration.

Cython bindings and Python interface to Opal, a SIMD-accelerated database search aligner.