bioinformatics

Common Workflow Language - computational workflows @ UNLOCK

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

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

DElite is a novel R package for DE analysis. With a single command line, DE returns the output of edgeR, limma, dearseq and DESeq2, both as individual results and as a combined output. DElite offers user-friendly functionality, accompanied by a detailed report, and allows advanced users to customize their analyses to a high degree.

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

Proteinortho is a tool to detect orthologous genes within different species. (Download)

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.

Compute phylogenetic trees from distance matrix using BioNJ algorithm. It will produce Newick file and Weighted newick if needed. There is also a render using Equal-angle algorithm and SVG output for testing. It's preferred to use a JS render like 'phylotree.js' (demo of phylotree.js here http://phylotree.hyphy.org/).

DAPCy is a Python implementation of the Discriminant Analysis of Principal Components (DAPC) method for population genetics.

https://uhasselt-bioinfo.gitlab.io/dapcy/

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

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).

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

SonicParanoid is a stand-alone software tool for the identification of orthologous relationships among multiple species.

For details go to the wiki-page

Software to compute the melting temperature of nucleic acid duplexes

SeqExtract searches annotated genomes for keywords and extract corresponding fasta records

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

https://dnarna.gitlab.io/ampcheck

A plugin for Qiime2 to trim oligonucleotides and reverse-complement reads

Genome partitioning utilities