Bioinformatics Laboratory

All

23 repositories

ansible
Public
Barbera van Schaik, public repo for installation scripts virtual machines
Shell
•
GNU General Public License v3.0
•0•1•3•0•Updated Feb 18, 2026Feb 18, 2026
AHK_scripts
Public
Antoine van Kampen: Auto Hotkey Scripts
autohotkey ahk
AutoHotkey
•
GNU General Public License v3.0
•0•0•0•0•Updated Nov 24, 2025Nov 24, 2025
ENCORE
Public
ENCORE: Enhancing Computational Reproducibility
science bioinformatics research reproducible-research reproducible-science computational reproducibility encore computational-modelling
Python
•
Other
•3•11•8•0•Updated Oct 17, 2025Oct 17, 2025
prtools
Public
Yiting Shen, Perry Moerland: PRTools for Python
python machine-learning
Python
•19•0•0•0•Updated Oct 13, 2025Oct 13, 2025
Robustness_evaluation_deconv_methods
Public
Utkarsh Mahamune, Aldo Jongejan, Antoine van Kampen and Perry D Moerland: Systematic evaluation of robustness to cell type mismatch of deconvolution methods for…
benchmarking single-cell encore spatial-transcriptomics deconvolution-methods
R
•
GNU General Public License v3.0
•3•0•1•0•Updated Aug 12, 2025Aug 12, 2025
macrophage_sc_analysis
Public
Philip Ahmadzada, Perry Moerland: Comparative single-cell analysis of macrophages and macrophage subtypes in atherosclerotic mice and humans
Jupyter Notebook
•
GNU General Public License v3.0
•1•0•0•0•Updated Jun 24, 2025Jun 24, 2025
Benchmarking_ST_Deconvolution
Public
Aryamaan Bose, Utkarsh Mahamune, Perry Moerland: Benchmarking reference-based deconvolution methods for spatial transcriptomics data
HTML
•
GNU General Public License v3.0
•1•0•0•0•Updated Dec 18, 2024Dec 18, 2024
scRNASeq_analysis_ANCA
Public
Akdo Jongejan, Perry Moerland: Main scripts used in the analysis of the single-cell RNA-seq data of ANCA-associated glomerulonephritis as described in Vegting e…
support single-cell-rna-seq
R
•
GNU General Public License v3.0
•1•0•0•0•Updated Sep 23, 2024Sep 23, 2024
ENCORE_AUTOMATION
Public
ENCORE_AUTOMATION
github automation reproducible-research reproducible-science computational reproducibility encore
HTML
•
Other
•1•0•1•0•Updated Sep 18, 2024Sep 18, 2024
ENCORE-SUPPLEMENT
Public
ENCORE Supplementary Material
reproducible-research computational reproducibility encore computational-research
Other
•1•1•1•0•Updated Sep 17, 2024Sep 17, 2024
FSS-Navigator
Public
Antoine van Kampen, Aldo Jongejan, Utkarsh Mahamune: The standardized file system structure (FSS) navigator
reproducible-research navigator encore directory-traversal fss reproducible-support
HTML
•
GNU General Public License v3.0
•2•0•11•0•Updated Aug 1, 2024Aug 1, 2024
zenodo-test-bvs
Public
Test repo to see if a release is automatically added to Zenodo
Shell
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 29, 2024Jul 29, 2024
reseda
Public
Barbera van Schaik, Antoine van Kampen: REpertoire SEquence Data Analysis
support bioinformatics pipeline immunology repertoire-analysis airr-seq repertoire-sequencing
Jupyter Notebook
•0•1•0•0•Updated Jun 12, 2024Jun 12, 2024
ENCORE-AIRRseq-TEMPLATE
Public
Barbera van Schaik, Antoine van Kampen: ENCORE project for analysis for T-cell and B-cell repertoires
bioinformatics reproducibility encore repertoire-analysis airr-seq repertoire-sequencing reseda airrseq
Python
•
Other
•0•1•0•0•Updated May 31, 2024May 31, 2024
PhDthesisUmeshNandal
Public
Umesh Nandal, Perry Moerland: additional files for chapters 4 and 5 of the PhD thesis of Umesh Nandal
research thesis
GNU General Public License v3.0
•0•0•0•0•Updated Aug 5, 2023Aug 5, 2023
Clonal_aRt_visualization
Public
Rodrigo Garcia Valiente: Visual artsy representation of B-cell clonal repertoires using R
visualization r clone antibody airr-seq repertoire-sequencing
R
•
GNU General Public License v3.0
•0•0•0•0•Updated Jun 16, 2023Jun 16, 2023
scRNAseqVisualization
Public
Tobias Beers, Perry Moerland: MSc Computational Science project on (hierarchical) PPCA-techniques for scRNA-seq data.
visualization education scrna-seq probabilistic-programming stan
Jupyter Notebook
•
GNU General Public License v3.0
•1•0•0•0•Updated Apr 16, 2023Apr 16, 2023
BCRCF
Public
Dasha Balashova, Antoine van Kampen, Barbera van Schaik: BCRCF
airr-seq bcell clonalfamily
Jupyter Notebook
•
GNU General Public License v3.0
•0•0•0•0•Updated Feb 27, 2023Feb 27, 2023
GC_ABM_SHM_network
Public
Rodrigo García-Valiente, Elena Merino, Antoine van Kampen. ABM of the germinal center with implementation of SHM fate tree, sequence representation and PC/MBC g…
abm gc research-project grn
Standard ML
•1•0•0•0•Updated Jul 20, 2022Jul 20, 2022
ComputingInR
Public
Perry Moerland: Teaching material for the course Computing in R
education xaringan graduate-school
HTML
•
GNU General Public License v3.0
•1•0•0•0•Updated Jan 7, 2022Jan 7, 2022
GC_from_Affinity_to_Kinetics
Public
Standard ML
•0•0•0•0•Updated Sep 21, 2021Sep 21, 2021
AsymmetricDivision
Public
Elena Merino, Antoine van Kampen: Mafalda simulation of the germinal center. The effect of asymmetric cell division on plasma cell differentiation.
research simulation agent-based-modeling plasma-cell-differentiation
Standard ML
•
GNU General Public License v3.0
•0•0•0•2•Updated May 28, 2021May 28, 2021
MSM_PCdifferentiation
Public
Elena Merino Tejero, Antoine van Kampen: Multiscale model of plasma cell differentiation
research abm ode gc immunology multi-scale gene-regulatory-network plasma-cell plasma-cell-differentiation
Standard ML
•
GNU General Public License v3.0
•0•0•0•0•Updated Jan 27, 2021Jan 27, 2021