Leiden University Medical Center

pytest-workflow

Configure workflow/pipeline tests using yaml files.

EfDS

Materials for Essentials for Data Science, a course of Statistics and Data Science master at Leiden University.

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.

dgeAnalysis

R package with Shiny application for DGE analysis

fastq-filter

A fast FASTQ filter program.

HAMLET

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

rcourse

Using R for Data Analysis

EfDS_DB

Essentials for Data Science: 3*4h course on relational databases

hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics

slurm-cluster-status

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

Argalaxy-ImmuneRepertoire

Argalaxy Immune Repertoire pipeline

array-as-vcf

FAIRDataPoint

Fork of the FAIR Data Point repository, collecting changes and issues with the FDP implementation at the LUMC.

pgx-variant-tools

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

python-course

vtools

Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed

ansible-galaxy-cluster

Ansible role for installing galaxy on a node connected to a cluster.

docker-galaxy-uwsgi

freebayes-snakemake

Short read pipeline using bwa-mem2, freebayes and whatshap to call phased variants

haploblock-combiner

Generate all possible combinations between phased haploblocks

KeyGenes-dataprocessor

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

PacBio-variantcalling

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

RPCA

RNA-seq pipeline comparison and analyses

shm_csr

Somatic hypermutation and class switch recombination pipeline

SSLP-Analyzer

vcfphasesets

Get variants as phase sets from a VCF file using pysam.