Pinned Repositories
dgeAnalysis
R package with Shiny application for DGE analysis
EfDS
Materials for Essentials for Data Science, a course of Statistics and Data Science master at Leiden University.
EfDS_DB
Essentials for Data Science: 3*4h course on relational databases
fastq-filter
A fast FASTQ filter program.
fastqsplitter
Splits fastq files evenly
galaxy-launcher
A project to launch the galaxy docker image easily using ansible
HAMLET
RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
kPAL
Analysis toolkit and programming library for k-mer profiles
pytest-workflow
Configure workflow/pipeline tests using yaml files.
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.
Leiden University Medical Center's Repositories
LUMC/pytest-workflow
Configure workflow/pipeline tests using yaml files.
LUMC/EfDS
Materials for Essentials for Data Science, a course of Statistics and Data Science master at Leiden University.
LUMC/dgeAnalysis
R package with Shiny application for DGE analysis
LUMC/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.
LUMC/fastq-filter
A fast FASTQ filter program.
LUMC/HAMLET
RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
LUMC/EfDS_DB
Essentials for Data Science: 3*4h course on relational databases
LUMC/rcourse
Using R for Data Analysis
LUMC/slurm-cluster-status
Little tool for snakemake's --cluster-status argument for use with SLURM
LUMC/Argalaxy-ImmuneRepertoire
Argalaxy Immune Repertoire pipeline
LUMC/array-as-vcf
LUMC/FAIRDataPoint
Fork of the FAIR Data Point repository, collecting changes and issues with the FDP implementation at the LUMC.
LUMC/pgx-variant-tools
This library contains various methods and utilities for the calling and manipulation of normalized variants.
LUMC/python-course
LUMC/vtools
Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed
LUMC/ansible-galaxy-cluster
Ansible role for installing galaxy on a node connected to a cluster.
LUMC/barend-botje
Project set up for the retirement of Barend Mons.
LUMC/docker-galaxy-uwsgi
LUMC/freebayes-snakemake
Short read pipeline using bwa-mem2, freebayes and whatshap to call phased variants
LUMC/haploblock-combiner
Generate all possible combinations between phased haploblocks
LUMC/KeyGenes-dataprocessor
LUMC/lumc-galaxy-tools
Tools developed for use on LUMC's galaxy instance
LUMC/miniwdl-slurm
Extends miniwdl to run workflows on SLURM clusters in singularity containers.
LUMC/MRN-browser
LUMC/MultiQC_PGx
MultiQC plugin for the LUMC PGx project
LUMC/PacBio-variantcalling
Variant calling workflow for PacBio HiFi data. Part of the LUMC PGx project.
LUMC/RPCA
RNA-seq pipeline comparison and analyses
LUMC/shm_csr
Somatic hypermutation and class switch recombination pipeline
LUMC/SSLP-Analyzer
LUMC/vcfphasesets
Get variants as phase sets from a VCF file using pysam.