Pinned Repositories
ELAN_tools
Utility scripts for elabjournal
GenotoxicEcoli
MutationalPatterns
R package for extracting and visualizing mutational patterns in base substitution catalogues
MutSigPipe
Mutational signature selection and refitting pipeline
NF-IAP
Illumina Analysis Pipeline in Nextflow
NF-SMuRF
Somatic Mutations Rechecker and Filtering
PrimerDesign
Tool to design primers on a vcf file (using primer3 software)
PTATO
PTa Analysis TOolkit
RNASeq-NF
RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.
SMuRF
Somatic Mutations Rechecker and Filtering
Team van Boxtel @ Princess Maxima Center's Repositories
ToolsVanBox/PTATO
PTa Analysis TOolkit
ToolsVanBox/MutationalPatterns
R package for extracting and visualizing mutational patterns in base substitution catalogues
ToolsVanBox/PrimerDesign
Tool to design primers on a vcf file (using primer3 software)
ToolsVanBox/SMuRF
Somatic Mutations Rechecker and Filtering
ToolsVanBox/NF-IAP
Illumina Analysis Pipeline in Nextflow
ToolsVanBox/ELAN_tools
Utility scripts for elabjournal
ToolsVanBox/GenotoxicEcoli
ToolsVanBox/Genotoxin_assay
Data and code accompanying the research protocol: "Assessing the mutagenic impact of genotoxins in human umbilical cord-blood derived stem cells"
ToolsVanBox/Identify_lowVAF_bulk_muts
Identify mutations that are clonally present in a clone but subclonally present in a bulk sample
ToolsVanBox/MutSigPipe
Mutational signature selection and refitting pipeline
ToolsVanBox/NF-SMuRF
Somatic Mutations Rechecker and Filtering
ToolsVanBox/RNASeq-NF
RNASeq-NF is an NGS analysis pipeline for RNA expression quantification.
ToolsVanBox/Target_capture_tools
Scripts to analyze targeted sequencing data
ToolsVanBox/CallableLoci_processor
Combines CallableLoci bed files from control and experimental samples.
ToolsVanBox/filterSomatic
Filter SNVs or Indels based on non genotype specific quality parameters.
ToolsVanBox/IAP
Illumina analysis pipeline
ToolsVanBox/INDELFI
Script for INDEL filtering
ToolsVanBox/Mutation_accumulation_T21
ToolsVanBox/Mutational_signature_refitting
Scripts to perform mutational signature refitting
ToolsVanBox/MutationalPatterns_manuscript2_data_scripts
ToolsVanBox/smMIPfil
script for smMIP data analysis
ToolsVanBox/SNVFI
Single Nucleotide Variant Filtering
ToolsVanBox/VAFchecker
ToolsVanBox/Walker
Link germline mutations with somatic variants