Discover UMCUGenetics/USEQ_tools Open Source project

An R package for predicting HR deficiency from mutation contexts

CHORD

NextflowModules

UMCU Genetics Nextflow modules

Illumina analysis pipeline

IAP

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

PolarMorphism

primary-met-wgs-comparison

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

Jupyter Notebook

hpcguix-web

The code that drives https://hpc.guix.info/browse.

JavaScript

COLO829_somaticSV

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

An R package for extracting mutational signatures from vcf files

mutSigExtractor

vcf-explorer

Database and interface for vcf files.

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

guix-additions

Scheme

RNASeq-NF

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

sparqling-genomics

SHARC

Genome Diagnostics Nextflow WES workflow

DxNextflowWES

scripts and tools for exomedepth based pipeline

exomedepth_scripts

AdvancedBioinformaticsCourse

ExonCov

ExonCov: Exon coverage statistics from BAM files

Predicting tumor type using WGS derived features

cuplr

CWL-CommandLineTools

UMCU Genetics CWL CommandLineTools

tumps: tumor purity simulation

tumps

CWL

CWL workflows

Resources used in diagnostics pipelines

Dx_resources

Cyclomics consensus pipeline based on LAST and dagcon

Cyclomics_consensus_pipeline

GATK QScripts used in our illumina variant calling pipeline.

GATK-QScripts

Scala

Complex_SVs

SNVFI

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

Genetic-Immune-Escape

Jupyter Notebook

cwl-atacseq

cwl implementation of the ATAC-seq pipeline

A python based approach to processing MC4C data

Dx_tracks

Verilog

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

fingerprint_workflow

Comparison of workflow languages using the DX mip fingerprint pipeline.

Small tools for genetics research

SmallTools

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

CyclomicsManuscript

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.

mltoolkit

SyNet

Synergistic pair detection

MATLAB

geneDriverAnnotator

Roff

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

FairDNA

Code from the DNA group developed during FAIR BYOD.

example data belonging to MutationalPatters package

MutationalPatterns-data

targetclone

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

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

hmfGeneAnnotation

smk-gwcyclomicsseq

snakemake pipeline for genome-wide cyclomics data processing

VariantFiltering

clarity_epp

Clarity LIMS epp scripts

Genome Diagnostics Genealogy

DxGenealogy

mips

Scripts/tools for working with mip experiments.

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

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.