bioinformatics

Local haplotype expression analysis

Single Nucleotide Allele Counting

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

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.

Trimming, alignment and variant identification tool. Made to help professional make a quick variant identification through an easy to follow user interface developed in R with the Shiny framework.

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

Environment-dependent evolution of digital organisms simulator.

Plynk is a Python wraper for the PLINK software plus some convenience tools to enable a seamless workflow of Plink in Python.

practice tasks for "Algorithms for Sequence Analysis"

Bioinformatics in Python - DNA Toolkit YouTube Channel: https://t.ly/RdzG3

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 v2.0. A Python version of the code is present in version 1.2.

Nextflow pipeline for DamID analysis

Tavit (Trimming, Alignment and Variant Identification Tool) pipeline made in Python with Anaconda.

Join On Integers

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