UMCUGenetics/dIEM

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R
License
MIT License
Created almost 4 years ago
Updated over 1 year ago

UMCUGenetics/dIEM

UMCUGenetics

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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.

MutationalPatterns

R package for extracting and visualizing mutational patterns in base substitution catalogues

RNASeq

RNASeq pipeline

CHORD

An R package for predicting HR deficiency from mutation contexts

NextflowModules

UMCU Genetics Nextflow modules

IAP

Illumina analysis pipeline

PolarMorphism

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

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.

COLO829_somaticSV

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

mutSigExtractor

An R package for extracting mutational signatures from vcf files

vcf-explorer

Database and interface for vcf files.

guix-additions

RNASeq-NF

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

sparqling-genomics

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

SHARC

DxNextflowWES

Genome Diagnostics Nextflow WES workflow

exomedepth_scripts

scripts and tools for exomedepth based pipeline

AdvancedBioinformaticsCourse

ExonCov

ExonCov: Exon coverage statistics from BAM files

cuplr

Predicting tumor type using WGS derived features

CWL-CommandLineTools

UMCU Genetics CWL CommandLineTools

Common Workflow Language

tumps

tumps: tumor purity simulation

CWL

Common Workflow Language

Dx_resources

Resources used in diagnostics pipelines

Cyclomics_consensus_pipeline

Cyclomics consensus pipeline based on LAST and dagcon

GATK-QScripts

GATK QScripts used in our illumina variant calling pipeline.

Complex_SVs

SNVFI

Genetic-Immune-Escape

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

Jupyter Notebook

cwl-atacseq

cwl implementation of the ATAC-seq pipeline

Dx_tracks

pymc4c

A python based approach to processing MC4C data

bamMetrics

Tool to generate bam statistics and pdf/html reports.

NF-IAP

Illumina Analysis Pipeline in Nextflow

vcf-explorer_old

Vcf-explorer using couchDB - deprecated

GeoMx-DSP-analyses

Useq GeoMX DSP pipeline revision

DIMS

Direct Infusion Mass Spectrometry pipeline

USEQ_tools

Utility scripts to work with Genologics Clarity LIMS

fingerprint_workflow

Comparison of workflow languages using the DX mip fingerprint pipeline.

SmallTools

Small tools for genetics research

CyclomicsManuscript

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

mltoolkit

SyNet

Synergistic pair detection

geneDriverAnnotator

CWL-IAP

CWL workflow implementation of IAP.

Common Workflow Language

RNASeq-CWL

CWL implementation of the UMCU/RNASeq pipeline

Common Workflow Language

Pancreas_biobank

illumina-runinfo

Illumina runinfo web tool

guix-workflows

Workflows for the GWL

VirusSeq-CLI

CLI wrapper for the VirusSeq pipeline

BachelorBfx

ipython notebooks for Bachelor course bioinformatics

Jupyter Notebook

FairDNA

Code from the DNA group developed during FAIR BYOD.

MutationalPatterns-data

example data belonging to MutationalPatters package

targetclone

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

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

DxGenealogy

Genome Diagnostics Genealogy

mips

Scripts/tools for working with mip experiments.

ONCODE_MC

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).

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.