dupRadar is an R package which is part of the Bioconductor project . It requires mapped, duplicate marked RNA-Seq reads as a bam file and a gene annotation file in GTF format and produces a table with per gene values such as read counts, percentage of duplicate reads, normalized read counts. The package provides functions for plotting and analyzing the duplication rates dependent on the expression levels.

Install it from R with:

R> source("https://bioconductor.org/biocLite.R")
R> biocLite("dupRadar")

Features

  • RNA-Seq quality control
  • NGS PCR duplicate detection
  • Needs duplicate marked bam file and a reference GTF

Project Samples

Density of per gene duplication rates (good sample) Density of per gene duplication rates (problematic sample) Scatterplot of per gene duplication rate vs. expression / log10(RPK) on a dataset with a low amount of PCR artefacts. Boxplot of duplication rates of gene expression bins on a dataset with a low amount of PCR artefacts. Scatterplot of per gene duplication rate vs. expression / log10(RPK) on a dataset with a high amount of PCR artefacts. Boxplot of duplication rates of gene expression bins on a dataset with a high amount of PCR artefacts.

Project Activity

See All Activity >

Follow dupRadar

dupRadar Web Site

Other Useful Business Software
Fully Managed MySQL, PostgreSQL, and SQL Server Icon
Fully Managed MySQL, PostgreSQL, and SQL Server

Automatic backups, patching, replication, and failover. Focus on your app, not your database.

Cloud SQL handles your database ops end to end, so you can focus on your app.
Try Free
Rate This Project
Login To Rate This Project

User Reviews

Be the first to post a review of dupRadar!

Additional Project Details

Registered

2013-11-27
Report inappropriate content