B

bioinformatics

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

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

For details go to the wiki-page

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

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

Common Workflow Language - computational workflows @ UNLOCK

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.

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 JavaScript conversion tool for Open Data Science URIs

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.

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)

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).

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