dupRadar statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Alignment evaluation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

dupRadar specifications

Information


Unique identifier OMICS_11420
Name dupRadar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data It requires a BAM file with mapped and duplicate marked reads, and a gene model in GTF format.
Operating system Unix/Linux, Mac OS
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.10.0
Stability Stable
Requirements
BiocStyle, rmarkdown, knitr, AnnotationHub, R(>=3.2.0), Rsubread(>=1.14.1)
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Sergi Sayols <>

Publication for dupRadar

dupRadar in publications

 (2)
PMCID: 5898914
PMID: 29561261
DOI: 10.7554/eLife.32332.045

[…] assembly grch38 and quantification of genes of ensembl release v88 was done using star (v2.5.2b). duplicated reads were identified using picard markduplicates (v2.10.2) and were analyzed with dupradar (v1.6.0). differential gene expression analysis on raw counts was performed with deseq2 (v1.16.1). data were screened for protein-coding genes with higher expression in arg and/or brg […]

PMCID: 5726313
PMID: 29231921
DOI: 10.1038/sdata.2017.185

[…] quality metrics were calculated using the rnaseqc v1.18. following read alignment, duplication rates of the rna-seq samples were computed with bamutil v1.0.11 to mark duplicate reads and the dupradar v1.4 bioconductor r package for assessment. the gene expression profiles were quantified using cufflinks software version 2.2.1 to get the reads per kilobase of transcript per million mapped […]


To access a full list of publications, you will need to upgrade to our premium service.

dupRadar institution(s)
Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, Germany; FH Bingen, Germany; Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, Biberach an der Riß, Germany

dupRadar reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review dupRadar