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1. pdx_somatic_variant_calling pdx_somatic_variant_calling Public

   A containerized bioinformatics pipeline built with Nextflow to identify somatic (acquired) mutations in the tumor of patient-derived xenograft (PDX) models (currently tumor-only mode)

   Nextflow 3

2. vcf_expression_annotation vcf_expression_annotation Public

   Nextflow pipeline that annotates a VEP-annotated VCF file with transcript-level expression information using the vcf-expression-annotator tool from VAtools and performs some post-processing

   Nextflow

3. nextflow_purecn nextflow_purecn Public

   A nextflow pipeline to perform purecn

   Nextflow

4. nextflow_xengsort nextflow_xengsort Public

   A Nextflow pipeline to perform deconvolution of contaminant sequencing reads using Xengsort by Zentgraf and Rahmann (2021)

   HTML

5. samplesheet_generator_pdmr samplesheet_generator_pdmr Public

   Custom nextflow pipeline to produce samplesheets for my broader neoantigen prediction pipeline

   Nextflow 1

6. pili-lab-ub/pili_lab_website pili-lab-ub/pili_lab_website Public

   Website for the Roberto Pili Lab

   HTML