Malte Thodberg

multiomeR provides a reproducible R pipeline for analyzing large-scale single-nucleus Epi Multiome datasets, improving efficiency and reducing memory usage compared to existing workflows.

The paper introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

CAGEfightR is an R/Bioconductor package for analyzing CAGE data, enabling TSS and enhancer identification, annotation, quantification, and visualization.

This study provides a comprehensive TSS map for fission yeast under various stress and media conditions using CAGE, revealing new insights into gene regulation and promoter diversity.