UMCU Genetics

Repository for genetics code

Utrecht

Pinned Repositories

CHORD
An R package for predicting HR deficiency from mutation contexts
Language:R26 5 107
hpcguix-web
The code that drives https://hpc.guix.info/browse.
Language:JavaScript113
IAP
Illumina analysis pipeline
Language:Perl14 17 7915
MutationalPatterns
R package for extracting and visualizing mutational patterns in base substitution catalogues
Language:R103 9 7945
NextflowModules
UMCU Genetics Nextflow modules
Language:Nextflow25 11 610
NF-IAP
Illumina Analysis Pipeline in Nextflow
Language:Nextflow2 4 25
PolarMorphism
Discovery of genetic variants with shared effect across multiple phenotypes from GWAS summary statistics
Language:R11 4 91
primary-met-wgs-comparison
Code repo for all analysis done for the 'Pan-cancer whole genome comparison of primary and metastatic solid tumors' study.
Language:Jupyter Notebook12 5 03
RNASeq
RNASeq pipeline
Language:Perl35 12 519
RNASeq-NF
RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.
Language:Nextflow7 4 148

UMCU Genetics's Repositories

UMCUGenetics/NextflowModules
UMCU Genetics Nextflow modules
Language:Nextflow25 11 610
UMCUGenetics/hpcguix-web
The code that drives https://hpc.guix.info/browse.
Language:JavaScript113
UMCUGenetics/DxNextflowWES
Genome Diagnostics Nextflow WES workflow
Language:Nextflow6 10 141
UMCUGenetics/AdvancedBioinformaticsCourse
4 4 00
UMCUGenetics/ExonCov
ExonCov: Exon coverage statistics from BAM files
Language:Python4 11 293
UMCUGenetics/Dx_resources
Resources used in diagnostics pipelines
Language:Python3 12 530
UMCUGenetics/DIMS
Direct Infusion Mass Spectrometry pipeline
Language:R2 10 332
UMCUGenetics/Dx_tracks
Language:Verilog2 11 20
UMCUGenetics/USEQ_tools
Utility scripts to work with Genologics Clarity LIMS
Language:Python2 6 1
UMCUGenetics/clarity_epp
Clarity LIMS epp scripts
Language:Python1 10 150
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).
Language:HTML1 5 03
UMCUGenetics/clarity_portal
Clarity LIMS portal app
Language:Python0 8 30
UMCUGenetics/CustomModules
Language:R0 5 00
UMCUGenetics/DxNextflowWGS
Genome Diagnostics Nextflow WGS workflow
Language:Nextflow0 9 20
UMCUGenetics/alissa_interpret_client
Alissa Interpret Public API Client
Language:Python
UMCUGenetics/DIMSdb
database for Direct Infusion Mass Spectrometry pipeline
7 0
UMCUGenetics/DIMSpect_GUI
0 0
UMCUGenetics/DxNextflowFP
Repo with scripts to process fingerprint data.
1 0
UMCUGenetics/DxNextflowRNA
Language:R7 0
UMCUGenetics/Epi2Me_wf-human-variation
UMCUGenetics/franklin_client
Python package for Franklin API
1 0
UMCUGenetics/GIABEval
Genome-in-a-bottle evaluation tool to determine statistics
4 0
UMCUGenetics/HapSMA
Nextflow Oxford Nanopore Technologies workflow for SMA dataprocessing
Language:Nextflow
UMCUGenetics/ManuscriptSMNGeneConversion
Scripts and files related to the SMN gene conversion manuscript
UMCUGenetics/NanoRCS
NanoRCS: Multimodal genome-wide cfDNA sequencing and analysis
Language:Python2
UMCUGenetics/nf-core_template
Minimal nf-core compatible workflow template.
Language:Nextflow
UMCUGenetics/rnaseq-voila
Jupyter Notebook / Voila App for analysis and filtering of RNA-Seq data for clinical genetics diagnostics
UMCUGenetics/rsync_to_rdisc
Daemon to rsync data from HPC to bgarray
Language:Python8 5
UMCUGenetics/vip
Variant Interpretation Pipeline
UMCUGenetics/VUSualizer
Language:HTML8 8