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cgis-as-markers

Files for the Paper "CpG-Islands as markers for Liquid Biopsies of Cancer patients."

chipseq_scripts_jq-fcpf

This repository contains scripts for ChIPseq analysis with various BioConductor packages, for the paper "Chem-CRISPR/dCas9FCPF - a platform for chemically induced epigenome editing".

crispromeskape

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

DNA LLM

dvq

A python library to quickly compare DNA sequences

evo

DNA foundation modeling from molecular to genome scale

gatkvariantcalling

Snakemake pipeline for variant calling using GATK

ionmob

An open-source prediction framework for peptide ion collision cross section (CCS) values with python.

irf4-in-treg-and-th17

Repository containing the scripts for data processing of our Paper "Unveiling IRF4-steered regulation of context-dependent effector programs in Th17 and Treg cells"

mamba_ssm

A simple implementation of [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://arxiv.org/abs/2312.00752)

mlm-pytorch

An implementation of masked language modeling for Pytorch, made as concise and simple as possible

netseekr

A networks analysis pipeline for RNASeq time series data

protein-lm-scaling

rasflow-visualize

RNA-Seq analysis workflow

snn-workshop-amld-2022

uvadlc_notebooks

Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2021/Spring 2022

vizzy

Plotting functions for genomics using ggplot2