TY  - JOUR
AU  - Ulrich, Elias
AU  - Pfister, Stefan M
AU  - Jäger, Natalie
TI  - Revana: a comprehensive tool for regulatory variant analysis and visualization of cancer genomes.
JO  - Bioinformatics
VL  - 39
IS  - 1
SN  - 0266-7061
CY  - Oxford
PB  - Oxford Univ. Press
M1  - DKFZ-2022-03214
SP  - btac831
PY  - 2023
N1  - #EA:B062#LA:B062# / 2023 Jan 1;39(1):btac831
AB  - As non-coding driver mutations move more into the focus of cancer research, a comprehensive and easy to use software solution for regulatory variant analysis and data visualization is highly relevant. The interpretation of regulatory variants in large tumor genome cohorts requires specialized analysis and visualization of multiple layers of data, including for example breakpoints of structural variants, enhancer elements and additional available gene locus annotation, in the context of changes in gene expression.We introduce a user-friendly tool, Revana (REgulatory Variant ANAlysis), that can aggregate and visually represent regulatory variants from cancer genomes in a gene-centric manner. It requires whole genome (WGS) and RNA sequencing (RNA-Seq) data of a cohort of tumor samples and creates interactive HTML reports summarizing the most important regulatory events.Revana is implemented in R and JavaScript. It is available for download as an R package under <https://github.com/KiTZ-Heidelberg/revana>. Sample results can be viewed under <https://github.com/KiTZ-Heidelberg/revana-demo-report> and a short walkthrough is available under <https://github.com/KiTZ-Heidelberg/revana-demo-data>.Supplementary data are available at Bioinformatics online.
LB  - PUB:(DE-HGF)16
C6  - pmid:36576005
DO  - DOI:10.1093/bioinformatics/btac831
UR  - https://inrepo02.dkfz.de/record/186493
ER  -