Discover UMCUGenetics/FairDNA Open Source project

UMCU Genetics Nextflow modules

NextflowModules

An R package for predicting HR deficiency from mutation contexts

CHORD

IAP

Illumina analysis pipeline

Discovery of genetic variants with shared effect across multiple phenotypes from GWAS summary statistics

PolarMorphism

vcf-explorer

Database and interface for vcf files.

Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.

primary-met-wgs-comparison

Jupyter Notebook

COLO829_somaticSV

Scripts and files used in the generation of the COLO829 somatic SV truthset.

The code that drives https://hpcguix.op.umcutrecht.nl.

guix-additions

Scheme

hpcguix-web

JavaScript

mutSigExtractor

An R package for extracting mutational signatures from vcf files

sparqling-genomics

Ontologies, RDF-generators, and a web interface for querying it all.

SHARC

RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.

RNASeq-NF

Genome Diagnostics Nextflow WES workflow

DxNextflowWES

scripts and tools for exomedepth based pipeline

exomedepth_scripts

AdvancedBioinformaticsCourse

ExonCov

ExonCov: Exon coverage statistics from BAM files

UMCU Genetics CWL CommandLineTools

CWL-CommandLineTools

tumps: tumor purity simulation

tumps

cuplr

Predicting tumor type using WGS derived features

GATK-QScripts

GATK QScripts used in our illumina variant calling pipeline.

Scala

CWL

CWL workflows

Resources used in diagnostics pipelines

Dx_resources

Cyclomics consensus pipeline based on LAST and dagcon

Cyclomics_consensus_pipeline

Complex_SVs

SNVFI

cwl implementation of the ATAC-seq pipeline

cwl-atacseq

A python based approach to processing MC4C data

pymc4c

Tool to generate bam statistics and pdf/html reports.

bamMetrics

Illumina Analysis Pipeline in Nextflow

NF-IAP

Vcf-explorer using couchDB - deprecated

vcf-explorer_old

ApacheConf

GeoMx-DSP-analyses

Useq GeoMX DSP pipeline revision

HTML

DIMS

Direct Infusion Mass Spectrometry pipeline

dIEM

For untargeted metabolomics, this tool calculates probability scores for metabolic disorders. In addition, it provides visual support with violin plots of the mass spectrometry (DI-HRMS) measurements for the lab specialists.

USEQ_tools

Utility scripts to work with Genologics Clarity LIMS

Comparison of workflow languages using the DX mip fingerprint pipeline.

fingerprint_workflow

Source code of the manuscript "Genetic immune escape landscape in primary and metastatic tumors"

Genetic-Immune-Escape

Jupyter Notebook

SmallTools

Small tools for genetics research

Data analysis scripts used to process and plot the data for the manuscript of CyclomicsSeq.

CyclomicsManuscript

mltoolkit

SyNet

Synergistic pair detection

MATLAB

geneDriverAnnotator

Roff

Dx_tracks

Verilog

CWL-IAP

CWL workflow implementation of IAP.

CWL implementation of the UMCU/RNASeq pipeline

RNASeq-CWL

Illumina runinfo web tool

Pancreas_biobank

illumina-runinfo

CLI wrapper for the VirusSeq pipeline

guix-workflows

Workflows for the GWL

Scheme

VirusSeq-CLI

ipython notebooks for Bachelor course bioinformatics

BachelorBfx

Jupyter Notebook

mips

Scripts/tools for working with mip experiments.

example data belonging to MutationalPatters package

MutationalPatterns-data

targetclone

TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors

Course materials for Oncode Masterclass: Introduction to machine learning in cancer genomics on the 18th November 2020 by Jeroen de Ridder's group (UMC Utrecht) in collaboration with Lodewyk Wessel and Soufiane Mourragui (NKI).

ONCODE_MC

HTML

hmfGeneAnnotation

Determines the biallelic status of selected genes using SNV, indel and CNV data

smk-gwcyclomicsseq

snakemake pipeline for genome-wide cyclomics data processing

VariantFiltering

clarity_epp

Clarity LIMS epp scripts

Genome Diagnostics Genealogy

DxGenealogy

CaddAnnotation

The CADD annotation pipeline annotates the contents of a tab-delimted database into an input VCF (in the INFO field). The chunkscript is used to run the annotation script in parallel, to annotate faster.