Exome/Capture/RNASeq Pipeline Implementation using snakemake

The snakemake workflow for whole-exome sequencing analysis and generating vcf files

DNA and RNA variant calling pipelines with HLA typing and Neoantigen predictions

The DKFZ alignment workflow plugin originally developed at the eilslabs

In this repository I backup the pipelines I write for the project I am involved

Multi-WES CLI client

Sample and variant quality control for WGS, WES, and genotyping array data: contamination checks, sex concordance, coverage validation, batch effects, and cross-platform concordance

Toll made with AI to help understanding DOTS in WES Pathways, thanks to Fibonacci. I use 23andme with ANNOVAR annotations files.

WES pipeline with customizable scoring system based on 10 criteria.

MAD-GE (Mutant Aware Deconvolution of Gene Expression) builds personalized transcriptomes to quantify mutant alleles from tumor bulk RNA-seq. Coded pre-LLM by a biologist without a strong CS background, this pipeline was recently refactored and tidied with Gemini to ensure transparency and reproducibility for publication.