Erasmus Medical Center

Bioinformatics Department

20 followers
Rotterdam, The Netherlands
https://erasmusmc-bioinformatics.github.io/

Overview
Repositories
Projects
Packages
People

Popular repositories Loading

WeFaceNano WeFaceNano Public

Nanopore plasmid pipeline (FAST5 basecalling, assembly, plasmid identification and antimicrobial resistance genes identification).

Python 13 1
benchAMRking benchAMRking Public

SCSS 4 1
galaxytools-emc galaxytools-emc Public

Tool Shed repositories maintained and developed by the Erasmus University Medical Center, following best practices guidelines set out by the Intergalactic Utilities Commission https://wiki.galaxypr…

Python 3 1
ARGalaxy-docker ARGalaxy-docker Public

Docker image that sets up a Galaxy with the Immune Repertoire and SHM pipelines.

HTML 3
molclass molclass Public

Moleculair classification tool, search for a variant and get results from many sources

Python 3 1
EMC-MetaMicrobes EMC-MetaMicrobes Public

Nextflow pipeline to detect and classify microbial reads in sequencing data from human samples.

Nextflow 3 2

Repositories

Type Language

Select language

All C++ CSS Dockerfile HTML JavaScript Jinja Jupyter Notebook Makefile Nextflow PHP Python R SCSS Shell TeX

Sort

spyCNV Public
A modern copy number variation (CNV) analysis tool that produces standalone interactive HTML reports from TSO500 sequencing data. Built with genome-spy, inspired by reconCNV. Usable as both a CLI and a Python library.

ErasmusMC-Bioinformatics/spyCNV's past year of commit activity

Jinja 0 0 0 0 Updated Aug 28, 2026
ecpc Public

ErasmusMC-Bioinformatics/ecpc's past year of commit activity

Makefile 0 0 0 0 Updated Aug 12, 2026
molclass Public
Moleculair classification tool, search for a variant and get results from many sources

ErasmusMC-Bioinformatics/molclass's past year of commit activity

Python 3 1 3 0 Updated Aug 4, 2026
src-component-pulsar Public
SRC Pulsar Component

ErasmusMC-Bioinformatics/src-component-pulsar's past year of commit activity

HTML 1 LGPL-2.1 1 0 1 Updated Jul 15, 2026
HMF-json2report Public
Create docx or txt reports from HMF json files. https://erasmusmc-bioinformatics.github.io/HMF-json2report/

ErasmusMC-Bioinformatics/HMF-json2report's past year of commit activity

HTML 0 0 0 0 Updated Jun 23, 2026
EMC-SigProfiler Public
A Python CLI tool and library built on top of SigProfiler for generating self-contained HTML reports from VCF's or TSV's.

ErasmusMC-Bioinformatics/EMC-SigProfiler's past year of commit activity

Python 0 0 0 0 Updated Jun 22, 2026
erasmusmc-bioinformatics.github.io Public
ErasmusMC Bioinformatics Landing Page

ErasmusMC-Bioinformatics/erasmusmc-bioinformatics.github.io's past year of commit activity

HTML 0 MIT 1 4 12 Updated Jun 5, 2026
Spatial-Cookbook Public
Useful scripts for processing and analyzing spatial omics data

ErasmusMC-Bioinformatics/Spatial-Cookbook's past year of commit activity

HTML 1 0 0 0 Updated May 27, 2026
AILMENT_ML_GUT Public
ML framework for metatranscriptomics and metagenomics for species and tumour traits

ErasmusMC-Bioinformatics/AILMENT_ML_GUT's past year of commit activity

Jupyter Notebook 0 0 0 0 Updated Mar 30, 2026
OrganoTrack Public
Image analysis pipeline of organoid images

ErasmusMC-Bioinformatics/OrganoTrack's past year of commit activity

Python 0 0 0 0 Updated Mar 17, 2026