Redmar-van-den-Berg

Bio-informatician with experience in microbiology and clinical genetics

Pinned Repositories

HAMLET
RNA-seq pipeline for AML diagnostics developed in collaboration with the LUMC Hematology department
Language:Python6 4 274
ansible-for-devops
Ansible examples from Ansible for DevOps.
Language:Python0 1 00
covid-variants-nl
Estimate the weekly number of COVID infections for each variant
Language:Python0 2 00
haploblock-shuffler
Shuffle phased and unphased variants
Language:Python0 2 00
HiFi-assembly
Assemble HiFi reads and identify genes of interest
Language:Python2 2 00
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
Language:JavaScript0 1 00
snakemake-module-example
Example of combining multiple Snakemake files as modules
Language:Python1 2 00
snakemake-project
Example of a snakemake project
Language:Python1 3 02

Redmar-van-den-Berg's Repositories

Redmar-van-den-Berg/HUMID
HUMID: reference free FastQ deduplication
Language:C++2 1 00
Redmar-van-den-Berg/snakemake-project
Example of a snakemake project
Language:Python1 3 02
Redmar-van-den-Berg/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
Language:JavaScript0 1 00
Redmar-van-den-Berg/arriba
Fast and accurate gene fusion detection from RNA-Seq data
Redmar-van-den-Berg/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell1 0
Redmar-van-den-Berg/dynamisch-tarief
API for dynamic energy prices in the netherlands
Language:Python2 0
Redmar-van-den-Berg/eido
Validator for PEP objects
Language:Python1 0
Redmar-van-den-Berg/exonviz
Visualise exons and their reading frames
Language:Python2 1
Redmar-van-den-Berg/exonviz-web
Web interface for Exonviz
Language:Python1 1
Redmar-van-den-Berg/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
Language:C++1 0
Redmar-van-den-Berg/GTGT
Genetic Therapy Generator Toolkit
Language:Python2 0
Redmar-van-den-Berg/HLA-typing
Language:Python
Redmar-van-den-Berg/kickstart.nvim
A launch point for your personal nvim configuration
Language:Lua1 0
Redmar-van-den-Berg/multi-package-containers
Testing building mulled containers for multi-requirement tools.
1 0
Redmar-van-den-Berg/MultiQC_TestData
Test data for MultiQC. See https://github.com/ewels/MultiQC
Language:HTML1 0
Redmar-van-den-Berg/NvChad
Blazing fast Neovim config providing solid defaults and a beautiful UI, enhancing your neovim experience.
Language:Lua1 0
Redmar-van-den-Berg/Posters
Language:TeX1 0
Redmar-van-den-Berg/pydantic
Data validation using Python type hints
Redmar-van-den-Berg/python-project
Language:Python2 0
Redmar-van-den-Berg/readthedocs-tutorial
Language:Python2 0
Redmar-van-den-Berg/reference-free-deduplication
Benchmark reference free UMI deduplication tools
Language:Python
Redmar-van-den-Berg/seAMLess
A single cell transcriptomics based deconvolution pipeline for Leukemia
Language:R1 0
Redmar-van-den-Berg/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
Language:HTML
Redmar-van-den-Berg/snakemake-tssv
Language:Python2 0
Redmar-van-den-Berg/somatic-RNA-variant-callers
Run multiple somatic RNA variant callers
Language:Python
Redmar-van-den-Berg/SpecHLA
SpecHLA reconstructs entire diploid sequences of HLA genes and infers LOH events. It supports HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1 genes. Also, it supports both short- and long-read data.
Language:C++0 0
Redmar-van-den-Berg/STAR_counts
Language:Python1 0
Redmar-van-den-Berg/test-umi-deduplication
Test umi deduplication with umi-tools and umi-trie
Language:Python2 0
Redmar-van-den-Berg/ucsc-playground
Messing around with the UCSC API
Language:Python2 0
Redmar-van-den-Berg/UMIc
A framework implementing a method for UMI deduplication and reads correction.
Language:R1 0