A QC pipeline for SVs calls based on coverage and SNP calls

Aggregation of QC metrics and outlier nomination for multi-sample studies

An assessment of the species diversity and disease potential of Pythium communities in Europe

Here is my participation to the 2024 edition of the HackBio Internship (AMR in cancer track).

This tool is aimed at helping to analyze small to medium vcf files of genotyped individuals.

Useful R-scripts by edert

Algorithm to implement Fraction and Allelic Copy number Estimate from Tumor/normal Sequencing using unmatched normal sample(s) for log ratio calculations

A repository for efficient population genomic analysis using Snakemake workflow.

Analysis of Single-Cell RNA data from SRR14294834 in peripheral blood mononuclear cells in severe asthma

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.

RNA-seq analysis workflow using DESeq2

Bioinformatics analysis pipeline for metagenomic profiling, functional annotation, and machine learning on T2D patient data.

ChIP-seq

Source code to support the paper: “Extensive tissue-specific expression variation and novel regulators underlying circadian behavior”

This project was my Master's (Biotechnology) Thesis project where we aimed to develop a machine learning model that identifies Oral cancer candidate genes.

Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"

Repository containing various RNA-seq, ChIP-seq, and 16S-seq analysis pipelines run through R

R Package for interrogating clonal data

a shiny frontend for the nextflow-bcl pipeline

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