C

computational biology

PlasBin-HMF is a CLI tool to perfom plasmid binning in short read assembly graph. It relies on a global optimization problem based on a multi-flow approach, where the flows on the arcs are proxy of the abundance of the DNA molecule in the sample.

BioFoundry is an open-source computational biology platform designed to streamline primer design, genome validation, and CRISPR-aware experiment planning. It combines traditional bioinformatics tools with modular, extensible architecture and AI-ready workflows to support researchers from raw DNA sequence input through to validated experimental design. Built under the AGPL-3.0+ license, it emphasizes transparency, reproducibility, and community-driven development — enabling collaborative innovation in modern genetic research. https://roxanneardary.com/biofoundry/

Language support for FASTA and FASTQ files in Gram and Zed.

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

https://dnarna.gitlab.io/ampcheck

SeqExtract searches annotated genomes for keywords and extract corresponding fasta records

CoNI is a practical R package for the unsupervised integration of numerical omics datasets. The tool is based on partial correlations to identify putative confounding variables for a set of paired dependent variables. CoNI combines two omics datasets in an integrated, complex hypergraph-like network, represented as a weighted undirected graph, a bipartite graph, or a hypergraph structure. These network representations form a basis for multiple further analyses, such as identifying priority candidates of biological importance or comparing network structures dependent on different conditions.

Development of a programme for the characterisation, data standardisation and comprehensive study of the properties of molecules/proteins.

RepeatGrower identify repeating k-mers in a genome and grows them until their occurrences decline.

Migrated to https://github.com/fpozoc/trifid

A computational model of non-photochemical quenching (NPQ) in diatoms. Part of a study testing the role and mechanism of K+ efflux antiporter 3 (KEA3) in photoprotection of diatoms.

Spatio-Temporal Antibiotic Resistance Adaptation Simulator

Some Bioinformatics example about dna, genes and other.

hiPathia is a methodology for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways