Muedi
Senior researcher @ DFKI - German Research Center for Artificial Intelligence. I am especially interested in genomics and machine learning.
DFKI
Pinned Repositories
learning-nucleotides
A comparison of next-token-prediction-Models for DNA sequences. We provide a new loss function to inform models of DNA 1D-topology.
autoTab
AutoML for TabData, Workshop poster
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.
qcGenes_manuscript
Workflows for correlation of Expression and peaks with file quality, related to our paper "Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets"
RASflow-visualize
RNA-Seq analysis workflow
protein-lm-scaling
seqQscorer
crispromeskape
Scripts to analyze the data for the paper "An outstanding bacterial membranome requires CRISPR-Cas systems to avoid the intervention of phages" and derive the figures or subfigures shown in the manuscript.
Muedi's Repositories
Muedi/CGIs-as-markers
Files for the Paper "CpG-Islands as markers for Liquid Biopsies of Cancer patients."
Muedi/autoTab
AutoML for TabData, Workshop poster
Muedi/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.
Muedi/RASflow-visualize
RNA-Seq analysis workflow
Muedi/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".
Muedi/DNA-LLM
DNA LLM
Muedi/dvq
A python library to quickly compare DNA sequences
Muedi/evo
DNA foundation modeling from molecular to genome scale
Muedi/ionmob
An open-source prediction framework for peptide ion collision cross section (CCS) values with python.
Muedi/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"
Muedi/qcGenes_manuscript
Workflows for correlation of Expression and peaks with file quality, related to our paper "Overlooked poor-quality patient samples in sequencing data impair reproducibility of published clinically relevant datasets"
Muedi/Expression-Analysis-in-r-and-Python
Scripts and Markdowns for the Expression Data of our Bachelor Module @ the Uni Mainz
Muedi/gatkVariantCalling
Snakemake pipeline for variant calling using GATK
Muedi/Mamba_SSM
A simple implementation of [Mamba: Linear-Time Sequence Modeling with Selective State Spaces](https://arxiv.org/abs/2312.00752)
Muedi/mlm-pytorch
An implementation of masked language modeling for Pytorch, made as concise and simple as possible
Muedi/NetSeekR
A networks analysis pipeline for RNASeq time series data
Muedi/protein-lm-scaling
Muedi/snn-workshop-amld-2022
Muedi/uvadlc_notebooks
Repository of Jupyter notebook tutorials for teaching the Deep Learning Course at the University of Amsterdam (MSc AI), Fall 2021/Spring 2022
Muedi/vizzy
Plotting functions for genomics using ggplot2