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/MutationalPatterns
R package for extracting and visualizing mutational patterns in base substitution catalogues
UMCUGenetics/CHORD
An R package for predicting HR deficiency from mutation contexts
UMCUGenetics/primary-met-wgs-comparison
Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.
UMCUGenetics/PolarMorphism
Discovery of genetic variants with shared effect across multiple phenotypes from GWAS summary statistics
UMCUGenetics/hpcguix-web
The code that drives https://hpc.guix.info/browse.
UMCUGenetics/COLO829_somaticSV
Scripts and files used in the generation of the COLO829 somatic SV truthset.
UMCUGenetics/RNASeq-NF
RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.
UMCUGenetics/SHARC
UMCUGenetics/cuplr
Predicting tumor type using WGS derived features
UMCUGenetics/tumps
tumps: tumor purity simulation
UMCUGenetics/Cyclomics_consensus_pipeline
Cyclomics consensus pipeline based on LAST and dagcon
UMCUGenetics/Genetic-Immune-Escape
Source code of the manuscript "Genetic immune escape landscape in primary and metastatic tumors"
UMCUGenetics/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.
UMCUGenetics/GeoMx-DSP-analyses
Useq GeoMX DSP pipeline revision
UMCUGenetics/NF-IAP
Illumina Analysis Pipeline in Nextflow
UMCUGenetics/ExomeDepth
ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
UMCUGenetics/smk-gwcyclomicsseq
snakemake pipeline for genome-wide cyclomics data processing
UMCUGenetics/DxNextflowMIP
Genome Diagnostics Nextflow MIP Fingerprint workflow
UMCUGenetics/DeeplexiconDemuxAndSplit
Wrapper pipeline script running demux and split on nanopore fast5 and fastq data using the Deeplexicon pipeline
UMCUGenetics/DIMS_Fragmentation
UMCUGenetics/Dx_BAF
UMCUGenetics/Dx_UPD
UMCUGenetics/EnsemblRest
A Python interface to the Ensembl REST APIs, biological data at your fingertips.
UMCUGenetics/FinalReport_filter
Software to filter Illumina Genomestudio FinalReport files
UMCUGenetics/IDT_SingleUMI_Pipeline
Pipeline for mapping of Fastq files with single UMI and first n nucleotides of the read
UMCUGenetics/qiseq_kcrbm
R code for Kernel Convolved Rule Based Mapping
UMCUGenetics/RNASeq_DE_Analysis
R-script pipeline for DE analysis of RNAseq data as generated by USEQ
UMCUGenetics/sarek_ubec
Slightly customized version of the Sarek pipeline. See sarek_ubec_documentation for details
UMCUGenetics/treatment_muts_healthy_tissue
code used to analyse anti cancer treatment mutations in healthy colon and liver adult stem cells
UMCUGenetics/Trend_Analysis_tool