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/vcf-explorer
Database and interface for vcf files.
UMCUGenetics/exomedepth_scripts
scripts and tools for exomedepth based pipeline
UMCUGenetics/Afib-Stroke-Overlap
Code and calls to software that accompanies manuscript on the overlap of atrial fibrillation genetics and cardioembolic stroke
UMCUGenetics/CWL
CWL workflows
UMCUGenetics/SNVFI
UMCUGenetics/bamMetrics
Tool to generate bam statistics and pdf/html reports.
UMCUGenetics/cwl-atacseq
cwl implementation of the ATAC-seq pipeline
UMCUGenetics/pymc4c
A python based approach to processing MC4C data
UMCUGenetics/SmallTools
Small tools for genetics research
UMCUGenetics/BachelorBfx
ipython notebooks for Bachelor course bioinformatics
UMCUGenetics/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.
UMCUGenetics/CWL-IAP
CWL workflow implementation of IAP.
UMCUGenetics/FairDNA
Code from the DNA group developed during FAIR BYOD.
UMCUGenetics/guix-workflows
Workflows for the GWL
UMCUGenetics/illumina-runinfo
Illumina runinfo web tool
UMCUGenetics/mips
Scripts/tools for working with mip experiments.
UMCUGenetics/Pancreas_biobank
UMCUGenetics/RNASeq-CWL
CWL implementation of the UMCU/RNASeq pipeline
UMCUGenetics/rostr
Multiplatform pipeline system for bio-informatic analysis
UMCUGenetics/SyNet
Synergistic pair detection
UMCUGenetics/VariantFiltering
UMCUGenetics/SAP42
contains legacy SOLID pipeline
UMCUGenetics/circular
:exclamation: This is a read-only mirror of the CRAN R package repository. circular — Circular Statistics
UMCUGenetics/Dansen
UMCUGenetics/dtwExtended
Extensions for the dtw package in R
UMCUGenetics/fatdistnGWAS
Code and data related to the meta-analysis of fat distribution in UK Biobank and GIANT
UMCUGenetics/IntroductionPython
Jupyter notebooks for the MSc introduction to python course
UMCUGenetics/Moldia
Replacement CPCTDB_web
UMCUGenetics/ShinyRNA
Shiny app to interact with basic RNAseq data
UMCUGenetics/UveitisJIA_MHC-fineMapping
Scripts and data used in analyses for "An amino acid motif in HLA-DRβ1 distinguishes patients with uveitis in juvenile idiopathic arthritis." Preprint: https://www.biorxiv.org/content/early/2017/08/14/140954