Docker to run TopHat for splice junction mapping

Different approaches to calculate mappability and GC-rich tracks for danio rerio genomes

A theme for Bowtie with a big 600px cover and CSS flip animation.

A reproducible RNA-Seq analysis pipeline for Staphylococcus aureus under antibiotic stress, utilizing Nextflow and Singularity. It involves genome mapping, read counting, and statistical analysis to identify differentially expressed genes (DEGs) and generates key visualizations.

This repository contains my end-of-degree project. I've implemented a simple version of three of the most known aligners like Bowtie, BWA and BWT-SM

Expanded version of the traditional Smith Waterman algorithm for local alignment

Code designed to run on Atom Computer's Tinker Tie. http://atomcomputer.us/tinkertie/

🔬 A replication of ChiP-Seq analysis from an experiment regarding gene induction and repression during terminal erythropoiesis that are mediated by distinct epigenetic changes

The project for the course "Web Information Retrieval"

A Nextflow pipeline that is designed to identify potential RNAi oligo candidates from a set of target genes and screen them for off-target effects by aligning them against a comprehensive reference genome or transcriptome.

Bowtie-based alignment of CRISPR gRNA spacer sequences

VAP : For Reference mapping and Variant detection.

A computational toolkit of fast and automatical identification of back-splice junctions of potential circular RNAs (circRNAs) from RNA-seq data.

Analyzing shotgun data

Tutorials for the crisprVerse

Nextflow Alignment Pipeline - from fastq.gz to sorted bam with ease

🌠 Easily download genomes and build BLAST/Bowtie indexes in Python

Detecting contamination in NGS data and multi-species analysis