Pinned Repositories
CHORD
An R package for predicting HR deficiency from mutation contexts
hpcguix-web
The code that drives https://hpc.guix.info/browse.
IAP
Illumina analysis pipeline
MutationalPatterns
R package for extracting and visualizing mutational patterns in base substitution catalogues
NextflowModules
UMCU Genetics Nextflow modules
NF-IAP
Illumina Analysis Pipeline in Nextflow
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.
RNASeq
RNASeq pipeline
RNASeq-NF
RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.
UMCU Genetics's Repositories
UMCUGenetics/Trend_Analysis_website
UMCUGenetics/Diseased_livers
Code and data for comparing mutation accumulation in alcoholic, NASH and PSC liver organoids
UMCUGenetics/SC_DNA-Aneufinder
Initial aneufinder SC DNA analysis script, made by E.W. Kuijk
UMCUGenetics/CoNVident
UMCUGenetics/geneDriverAnnotator
UMCUGenetics/sc-dna-pipeline
Single-cell DNA sequencing pipeline
UMCUGenetics/USCDtools
Characterization and quantification pipeline for copy number variation in single-cell sequencing data.
UMCUGenetics/cancer_type_classification_from_sparse_SNV_data
Scripts for processing and plotting data used in the 'Cancer type classification in liquid biopsies based on sparse mutational profiles enabled through data augmentation and integration' manuscript.
UMCUGenetics/guix-additions
UMCUGenetics/ELAN_tools
Utility scripts for elabjournal
UMCUGenetics/svMIL
Predicting pathogenic non-coding somatic SVs
UMCUGenetics/pcawg-analysis
Code for analyzing the PCAWG dataset using HMF pipeline v5.
UMCUGenetics/aneufinder
Find CNVs in single cell sequencing data.
UMCUGenetics/CyclomicsManuscript
Data analysis scripts used to process and plot the data for the manuscript of CyclomicsSeq.
UMCUGenetics/sgf-data-access-requirements
Web form to assign data access management to the DAC.
UMCUGenetics/ms-sjansen
UMCUGenetics/sparqling-genomics
Ontologies, RDF-generators, and a web interface for querying it all.
UMCUGenetics/DxGenealogy
Genome Diagnostics Genealogy
UMCUGenetics/pcawg-hmf-bacterial-integration
Bacterial integation analysis of PCAWG and HMF WGS donors.
UMCUGenetics/BLISS
BLISS analysis
UMCUGenetics/TRIBES
Finding cryptic relationships to boost disease gene detection
UMCUGenetics/mltoolkit
UMCUGenetics/NanoFG
Third-generation fusion gene detection
UMCUGenetics/hmfGeneAnnotation
Determines the biallelic status of selected genes using SNV, indel and CNV data
UMCUGenetics/OvCa_organoids_heterogeneity
Custom code for "Patient-derived ovarian cancer organoids mimic clinical response and exhibit heterogeneous inter- and intrapatient drug responses", De Witte et al . ADD REF!
UMCUGenetics/Crossomics
UMCUGenetics/IAP
Illumina analysis pipeline
UMCUGenetics/DIMS_GUI
R Shiny application to start the DIMS pipeline on the UMC HPC server
UMCUGenetics/in_vitro_mutational_load
Scripts for the the mutational impact of culturing human pluripotent and adult stem cells
UMCUGenetics/Complex_SVs