Detecting contamination in NGS data and multi-species analysis

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

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

Tutorials for the crisprVerse

Analyzing shotgun data

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

Bowtie-based alignment of CRISPR gRNA spacer sequences

VAP : For Reference mapping and Variant detection.

The project for the course "Web Information Retrieval"

The JSON Schema Ecosystem Observability Platform is a data-driven monitoring and analytics system designed to track the health, adoption, and compliance of the JSON Schema ecosystem.

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

For partial completion of AS.410.713.81.SP26, deep sequencing analysis is performed on paired end sequencing of Yersinia pestis first against a reference genome with bowtie using Bioconductor packages in R and then compared with de novo assembly using Velvet

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.

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.

Expanded version of the traditional Smith Waterman algorithm for local alignment

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

Docker to run TopHat for splice junction mapping

ML-powered Bowtie risk analysis for oil and gas incidents. Barrier failure prediction with XGBoost and SHAP, hybrid RAG over investigation reports, FastAPI + Next.js.