jdeligt Goto Github PK

advanced_bioinformatics_startercode

Repo for teaching purposes in the Advanced Bioinformatics course, UMC Utrecht, 2016

amrdetection

Project to learn some Rust and do on the fly AMR detection

analysis-workflows

Open workflow definitions for genomic analysis from MGI at WUSM.

beth-thesis

binding-site-predictor

Neural model to predict DNA binding sites of proteins

bioinformatics

Tools for bioinformatics

carpentries

Snippets relating the carpentries curriculum

chloroextractor

d3

D3 related documents and code

deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

diagnostics_exome_reporting

Pipeline to filter whole exome vcf files and generate a report document for clinical diagnostics.

fair_genomics_models

Semantic models generated during a BYOD for CancerGenomics.nl

frontline_genomics_presentation

Our presentation on 'real-time' genomics for ESR Data Science Week 2020.

guix-additions

human_genomics_pipeline

A simple Snakemake workflow to process paired-end sequencing data (WGS) using bwa/GATK4.

iap

Illumina variant calling pipeline

intro_python

Description introduction to python

jdeligt.github.io

Presentations, home page, blog & useful code snippets

licenses

Licenses approved by Team Digitale, ready to use in your repository

minimal-pathogen-agnostic-contextual-data-specification

An international minimal metadata standard for public health and One Health genomic surveillance.

ncov

Nextstrain build for novel coronavirus (nCoV)

pangenome-graphs-workshop

This repository contains material to construct pangenome graphs for a small bacteria dataset detailing every step in the Nesi environment.

pangenomegraph_microbe_paper

Paper writing for a first practical implementation of pangenome graph (pggb) for microbial genomics

python-novice-inflammation

Software Carpentry introduction to Python for novices using inflammation data.

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

sparqling-genomics

Ontologies, RDF-generators, and a web interface for querying it all.

strain-specific-unmapped-reads

Scripts and pipelines for the analysis of strain-specific unmapped reads in 31 rat-strains

tb

TB runs with nextstrain-augur

test-carpentry-python-2019

Workshop webpage

tools