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.
UMCUGenetics's Repositories
UMCUGenetics/NextflowModules
UMCU Genetics Nextflow modules
UMCUGenetics/mutSigExtractor
An R package for extracting mutational signatures from vcf files
UMCUGenetics/DxNextflowWES
Genome Diagnostics Nextflow WES workflow
UMCUGenetics/AdvancedBioinformaticsCourse
UMCUGenetics/ExonCov
ExonCov: Exon coverage statistics from BAM files
UMCUGenetics/Dx_resources
Resources used in diagnostics pipelines
UMCUGenetics/DIMS
Direct Infusion Mass Spectrometry pipeline
UMCUGenetics/Dx_tracks
UMCUGenetics/USEQ_tools
Utility scripts to work with Genologics Clarity LIMS
UMCUGenetics/clarity_epp
Clarity LIMS epp scripts
UMCUGenetics/CustomModules
UMCUGenetics/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).
UMCUGenetics/alissa_interpret_client
Alissa Interpret Public API Client
UMCUGenetics/clarity_portal
Clarity LIMS portal app
UMCUGenetics/DxNextflowWGS
Genome Diagnostics Nextflow WGS workflow
UMCUGenetics/rsync_to_rdisc
Daemon to rsync data from HPC to bgarray
UMCUGenetics/DIMSdb
database for Direct Infusion Mass Spectrometry pipeline
UMCUGenetics/DIMSpect_GUI
UMCUGenetics/DxNextflowFP
Repo with scripts to process fingerprint data.
UMCUGenetics/DxNextflowRNA
UMCUGenetics/Epi2Me_wf-human-variation
UMCUGenetics/franklin_client
Python package for Franklin API
UMCUGenetics/GIABEval
Genome-in-a-bottle evaluation tool to determine statistics
UMCUGenetics/HapSMA
Nextflow Oxford Nanopore Technologies workflow for SMA dataprocessing
UMCUGenetics/ManuscriptSMNGeneConversion
Scripts and files related to the SMN gene conversion manuscript
UMCUGenetics/NanoRCS
NanoRCS: Multimodal genome-wide cfDNA sequencing and analysis
UMCUGenetics/nf-core_template
Minimal nf-core compatible workflow template.
UMCUGenetics/rnaseq-voila
Jupyter Notebook / Voila App for analysis and filtering of RNA-Seq data for clinical genetics diagnostics
UMCUGenetics/vip
Variant Interpretation Pipeline
UMCUGenetics/VUSualizer