Automated analysis tool for mutations in promoters, transcription factor binding sites, coding regions and protein domains in the context of gene regulatory networks.

Code and scripts used for Worth et al. 2022: "Receptor editing constrains development of phosphatidyl choline-specific B cells in VH12-transgenic mice".

Whole exome sequencing snakemake workflow based on GATK best practice

main Repository for my Master's Thesis work

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

How to channel sequencing reads from multiple subdirectories into nextflow pipeline

Variant calling pipeline for Pacbio Hifi reads

HPV Pipeline (Human Papilloma Virus) is a bioinformatic pipeline designed to run Next-Generation Sequence reads to identify and genotype HPV infections in human specimens.

Variant Calling and Annotation using PacBio Hi-Fi Reads

Computational Suite For Bioinformaticians and Biologists (CSBB) provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. Providing User with End to End pipeline experience

SRSF framework for nucleosome positioning analysis

FASTQ read trimming by the highest scoring path algorithm

A tool for deep statistical analyses and informative visualizations of complex -omic data

List of sequencer runs; QC and run Info from each run, modular display of all existing (uploaded) types of info and statistics.

Trimming and QC on NGS data

Docker-based implementation of the Discover1.1 pipeline for bacterial characterization.

Code used to analyze and produce figures during tenure in the Translational Tumor Engineering Lab

Various bioinformatics tools in one package

HRV (human respiratory virus) Pipeline is a bioinformatic pipeline for the analysis of Illumina Next-Generation-Sequencing (NGS) for the discovery and GenBank submission of Human Respiratory Virus Genomes.