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hamlet

RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department

haploblock-combiner

Generate all possible combinations between phased haploblocks

hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics

keygenes-dataprocessor

kmer

Analysis toolkit and programming library for k-mer profiles (obsoleted by kPAL)

kpal

Analysis toolkit and programming library for k-mer profiles

locus_processing

Methods and tools for processing locus definition files.

lumc-galaxy-tools

Tools developed for use on LUMC's galaxy instance

miniwdl-slurm

Extends miniwdl to run workflows on SLURM clusters in singularity containers.

mrn-browser

multiqc_pgx

MultiQC plugin for the LUMC PGx project

nanopublication

ovogrowth-dataprocessor

pacbio-merge

Merge report files from PacBio tools

pacbio-variantcalling

Variant calling workflow for PacBio HiFi data. Part of the LUMC PGx project.

pgx-pipe-helper

Utility module to provide consistent handling of barcodes and loci by the PGx pipeline stages.

pgx-variant-tools

This library contains various methods and utilities for the calling and manipulation of normalized variants.

pigz-container

Docker container based on Debian buster containing pigz

prinia

Primer design tool

pytest-workflow

Configure workflow/pipeline tests using yaml files.

python-course

rcourse

Using R for Data Analysis

ribosome-profiling-analysis-framework

Ribosome profiling analysis framework as described in de Klerk E., Fokkema I.F.A.C et al (2015). Alignment, triplet periodicity analysis, detecting ORFs.

rna_cd

Detect RNA contamination in human Illumina DNA-seq experiments

rpca

RNA-seq pipeline comparison and analyses

sentinel

JSON-based QC database for NGS statistics

shm_csr

Somatic hypermutation and class switch recombination pipeline

singularity-recipes

Recipes for singularity containers used by LUMC analysis pipelines

slurm-cluster-status

Little tool for snakemake's --cluster-status argument for use with SLURM

sslp-analyzer