gerbenvoshol

T1K

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with RNA-seq, WGS or WES data.

gzinfo

gzinfo is a utility for inspecting and gathering information about gzip-compressed files.

tlock

Transparent Screen Lock Security software for Linux Systems

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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.

shvault

CLI secure shell/password vault

notebooks

containers

Bioinformatics containers

InterOpReader

Illumina InterOp File Reader

mscp

mscp: transfer files over multiple SSH (SFTP) connections

mjson

C/C++ JSON parser, emitter, JSON-RPC engine for embedded systems

FastqPuri

fastq quality assessment and filtering tool

miranda

[Tools] miRanda: An miRNA target scanner that aims to predict mRNA targets for microRNAs using dynamic-programming alignment and thermodynamics

passh

𝐬𝐬𝐡𝐩𝐚𝐬𝐬 is 𝒃𝒓𝒐𝒌𝒆𝒏 by design

md5tee

Program to calculate md5sum. Pipes data from stdin to stdout. Shows md5sum on stderr or file.

mkhtml

mkhtml is an html document generator that works with gpt

Squid

workshop-epigenomics-RTDs

workshop website on readthedocs

jstreeview

Interactive phylogenetic tree viewer/editor

ref-gen

Human reference genome analysis sets

MethylAid

IlluminaHumanMethylationEPICv2manifest

IlluminaHumanMethylationEPICv2anno.20a1.hg38

Stock-Prediction-Models

Gathers machine learning and deep learning models for Stock forecasting including trading bots and simulations

Statistics-Tool-Box

Single header file with a bunch of useful statistical functions such as ANOVA, Kruskal-Wallis, T-test, etc.

Dragen

Run Dragen as a container

AmpliCI

AmpliCI, a model-based algorithm for denoising Illumina amplicon data.

Mauve

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.

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: https://arxiv.org/abs/2211.08157).

peak-classifier

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF