bioinformatics

Common Workflow Language - computational workflows @ UNLOCK

OTP, One Touch Pipeline, Documentation at https://one-touch-pipeline.gitlab.io/otp/

A test GitHub repository for an R package (as part of the Scientific Programming exam).

A test GitHub repository for a set of client/server python scripts (as part of the Scientific Programming class).

Genome partitioning utilities

Local haplotype expression analysis

Single Nucleotide Allele Counting

Crawl any filesystem for genome data, providing one-click opening in IGV

Unix toolkit for feature analysis of alternative splicing events. Includes basic functions for manipulating tables, extraction of exon and intron-related features, discriminate feature analysis, motif maps for RNA-binding proteins, and more.

A tree-based orthology inference program with additional functionality for reducing contamination.

Environment-dependent evolution of digital organisms simulator.

Scripts for pathway enumeration and random flux sampling of metabolite exchanges in microbial models.

A d3 javascript SVG visualization of alternative splicing of randomly seeded exons from a random genome

Master thesis - Deep learning-based pairwise alignment of protein sequences using transformer architecture.

Run Oxford Nanopore MinION software in Docker containers

A Swiss Knife suite to manage pipeline environments