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    69 repositories

    • HAMLET

      Public
      RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
      Python
      •
      MIT License
      •4•6•2•0•Updated Nov 1, 2024Nov 1, 2024

    • barend-botje

      Public
      Project set up for the retirement of Barend Mons.
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 8, 2024Oct 8, 2024

    • rcourse

      Public
      Using R for Data Analysis
      R
      •
      GNU General Public License v3.0
      •1•4•7•0•Updated Sep 10, 2024Sep 10, 2024

    • pytest-workflow

      Public
      Configure workflow/pipeline tests using yaml files.
      testingyamlworkflowsnakemakepipelinenextflowtestpytestwdlpytest-plugin
      Python
      •
      GNU Affero General Public License v3.0
      •9•65•16•2•Updated Aug 4, 2024Aug 4, 2024

    • ansible-galaxy-cluster

      Public archive
      Ansible role for installing galaxy on a node connected to a cluster.
      Jinja
      •
      MIT License
      •0•0•0•1•Updated Jul 19, 2024Jul 19, 2024

    • EfDS

      Public
      Materials for Essentials for Data Science, a course of Statistics and Data Science master at Leiden University.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •27•17•0•0•Updated May 21, 2024May 21, 2024

    • docker-galaxy-uwsgi

      Public
      Dockerfile
      •
      MIT License
      •1•0•2•0•Updated Feb 14, 2024Feb 14, 2024

    • shm_csr

      Public
      Somatic hypermutation and class switch recombination pipeline
      R
      •
      MIT License
      •2•0•0•1•Updated Jan 10, 2024Jan 10, 2024

    • dgeAnalysis

      Public
      R package with Shiny application for DGE analysis
      R
      •
      MIT License
      •5•11•0•1•Updated Jan 8, 2024Jan 8, 2024

    • vcfphasesets

      Public
      Get variants as phase sets from a VCF file using pysam.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 5, 2024Jan 5, 2024

    • SSLP-Analyzer

      Public
      PHP
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Dec 12, 2023Dec 12, 2023

    • python-course

      Public
      Jupyter Notebook
      •5•1•0•8•Updated Nov 23, 2023Nov 23, 2023

    • MRN-browser

      Public
      HTML
      •0•0•0•0•Updated Nov 22, 2023Nov 22, 2023

    • slurm-cluster-status

      Public
      Little tool for snakemake's --cluster-status argument for use with SLURM
      snakemakeslurm
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•0•0•Updated Nov 22, 2023Nov 22, 2023

    • RPCA

      Public
      RNA-seq pipeline comparison and analyses
      Python
      •
      MIT License
      •1•0•0•2•Updated Sep 26, 2023Sep 26, 2023

    • vtools

      Public
      Various tools operating over VCF files. Uses cyvcf2 and cython under the hood for speed
      bioinformaticsvcfngs-analysisbioinformatics-tool
      Python
      •
      MIT License
      •1•1•1•0•Updated Aug 7, 2023Aug 7, 2023

    • ribosome-profiling-analysis-framework

      Public
      Ribosome profiling analysis framework as described in de Klerk E., Fokkema I.F.A.C et al (2015). Alignment, triplet periodicity analysis, detecting ORFs.
      PHP
      •
      Other
      •6•12•0•0•Updated May 16, 2023May 16, 2023

    • Argalaxy-ImmuneRepertoire

      Public
      Argalaxy Immune Repertoire pipeline
      R
      •
      MIT License
      •1•1•0•0•Updated Apr 21, 2023Apr 21, 2023

    • FAIRDataPoint

      Public
      Fork of the FAIR Data Point repository, collecting changes and issues with the FDP implementation at the LUMC.
      Java
      •
      MIT License
      •39•1•3•0•Updated Mar 13, 2023Mar 13, 2023

    • lumc-galaxy-tools

      Public
      Tools developed for use on LUMC's galaxy instance
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 13, 2023Jan 13, 2023

    • PacBio-variantcalling

      Public
      Variant calling workflow for PacBio HiFi data. Part of the LUMC PGx project.
      WDL
      •
      MIT License
      •0•0•0•0•Updated Nov 2, 2022Nov 2, 2022

    • MultiQC_PGx

      Public
      MultiQC plugin for the LUMC PGx project
      Python
      •0•0•0•0•Updated Oct 26, 2022Oct 26, 2022

    • KeyGenes-dataprocessor

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 18, 2022Oct 18, 2022

    • miniwdl-slurm

      Public archive
      Extends miniwdl to run workflows on SLURM clusters in singularity containers.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 30, 2022Aug 30, 2022

    • fastq-filter

      Public
      A fast FASTQ filter program.
      C
      •
      MIT License
      •3•6•0•0•Updated Aug 17, 2022Aug 17, 2022

    • array-as-vcf

      Public
      Python
      •
      MIT License
      •1•1•1•0•Updated Jul 15, 2022Jul 15, 2022

    • pgx-variant-tools

      Public
      This library contains various methods and utilities for the calling and manipulation of normalized variants.
      Python
      •
      MIT License
      •0•1•0•1•Updated Jun 22, 2022Jun 22, 2022

    • freebayes-snakemake

      Public
      Short read pipeline using bwa-mem2, freebayes and whatshap to call phased variants
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 21, 2022Jun 21, 2022

    • haploblock-combiner

      Public
      Generate all possible combinations between phased haploblocks
      Python
      •
      MIT License
      •0•0•1•0•Updated Mar 21, 2022Mar 21, 2022

    • EfDS_DB

      Public
      Essentials for Data Science: 3*4h course on relational databases
      Jupyter Notebook
      •11•4•0•0•Updated Mar 21, 2022Mar 21, 2022