Max Sprang's Projects
Files for the Paper "CpG-Islands as markers for Liquid Biopsies of Cancer patients."
This repository contains scripts for ChIPseq analysis with various BioConductor packages, for the paper "Chem-CRISPR/dCas9FCPF - a platform for chemically induced epigenome editing".
Scripts to analyze the data for the paper "Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems" and derive the figures or subfigures shown in the manuscript.
DNA LLM
A python library to quickly compare DNA sequences
DNA foundation modeling from molecular to genome scale
Snakemake pipeline for variant calling using GATK
An open-source prediction framework for peptide ion collision cross section (CCS) values with python.
Repository containing the scripts for data processing of our Paper "Unveiling IRF4-steered regulation of context-dependent effector programs in Th17 and Treg cells"
A simple implementation of [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://arxiv.org/abs/2312.00752)
An implementation of masked language modeling for Pytorch, made as concise and simple as possible
A networks analysis pipeline for RNASeq time series data
RNA-Seq analysis workflow
Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2021/Spring 2022
Plotting functions for genomics using ggplot2