Gerben Voshol's repositories
Statistics-Tool-Box
Single header file with a bunch of useful statistical functions such as ANOVA, Kruskal-Wallis, T-test, etc.
AmpliCI
AmpliCI, a model-based algorithm for denoising Illumina amplicon data.
containers
Bioinformatics containers
Dragen
Run Dragen as a container
fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
FastqPuri
fastq quality assessment and filtering tool
Genome-on-Diet
Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version:Β https://arxiv.org/abs/2211.08157).
gzinfo
gzinfo is a utility for inspecting and gathering information about gzip-compressed files.
InterOpReader
Illumina InterOp File Reader
jstreeview
Interactive phylogenetic tree viewer/editor
md5tee
Program to calculate md5sum. Pipes data from stdin to stdout. Shows md5sum on stderr or file.
miranda
[Tools] miRanda: An miRNA target scanner that aims to predict mRNA targets for microRNAs using dynamic-programming alignment and thermodynamics
mjson
C/C++ JSON parser, emitter, JSON-RPC engine for embedded systems
mkhtml
mkhtml is an html document generator that works with gpt
mscp
mscp: transfer files over multiple SSH (SFTP) connections
passh
π¬π¬π‘π©ππ¬π¬ is ππππππ by design
peak-classifier
Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
ref-gen
Human reference genome analysis sets
shvault
CLI secure shell/password vault
Stock-Prediction-Models
Gathers machine learning and deep learning models for Stock forecasting including trading bots and simulations
T1K
T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with RNA-seq, WGS or WES data.
tlock
Transparent Screen Lock Security software for Linux Systems
webui
Use any web browser as GUI, with your preferred language in the backend and HTML5 in the frontend, all in a lightweight portable lib.
workshop-epigenomics-RTDs
workshop website on readthedocs