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bioinformatics

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

A bioinformatic pipeline for identifying giant viruses and Preplasmiviricota viruses in metagenomic data.

Armadillo: fast C++ library for linear algebra (matrix maths) & scientific computing - https://arma.sourceforge.net

An implementation of Bayesian latent class model to estimate assays' performance with observed assay results, and latent true disease status.

BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures.

Matlab toolbox to generate xTop intensities from peptide-level intensities. It can also generate TopPepN (N=1,2,3..) intensities. The most updated version is v2.3 (March 2026). A Python version of the code is present in version 1.2, but its use is discouraged.

PDBNucleicAcids is a Biopython based package that constructs and represent all nucleic acids in a PDB structure, with a special focus on base-pair representation.

AmpCheck investigates primer/probe - template matching and return amplicon related information.

https://dnarna.gitlab.io/ampcheck

Common Workflow Language - computational workflows @ UNLOCK

Splicing analysis: Extract from mapped RNA-Seq-reads information on intron removal-order for exons genome-wide, and estimate their PSI values (percent-spliced-in) and PIR values (percent-intron-retention) of their flanking introns.

Automated drug repurposing workflow for rare diseases – using Flask, Monarch API, DGIdb API and XGboost.

Materials on various sections in Computer Science (CS). 🎓

🔬 Robust ML model selector with 95% CI guarantee for medical AI | Keratoconus detection achieving 84.3% recall, 3× variance reduction | Python/XGBoost | MIT License | Published research implementation 🏥📊

This repository provides a curated collection of datasets released for exploratory analysis, research, and reproducibility purposes.

The datasets included here are derived from public and/or processed sources and are published to support transparency, data reuse, and downstream analytical workflows such as exploration, feature engineering, and biomarker research.

Little utilities to work with fasta files.

A nextflow workflow to find Gene-Protein-Reaction relations

A workflow to identify gene-protein-reaction relations in Common Workflow Language

Software to compute the melting temperature of nucleic acid duplexes

SeqExtract searches annotated genomes for keywords and extract corresponding fasta records

Bioinformatics pipeline for LONELY gene family analysis across plant species