DupChecker

DOI: 10.18129/B9.bioc.DupChecker    

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see DupChecker.

a package for checking high-throughput genomic data redundancy in meta-analysis

Bioconductor version: Release (3.11)

Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data. Not removing duplicates would make study results questionable. We developed a Bioconductor package DupChecker that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data.

Author: Quanhu Sheng, Yu Shyr, Xi Chen

Maintainer: "Quanhu SHENG" <shengqh at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DupChecker")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DupChecker")

 

PDF	R Script	Validate genomic data with "DupChecker" package
PDF		Reference Manual

Details

biocViews	Preprocessing, Software
Version	1.25.0
In Bioconductor since	BioC 3.0 (R-3.1) (6 years)
License	GPL (>= 2)
Depends
Imports	tools, R.utils, RCurl
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DupChecker_1.25.0.tar.gz
Windows Binary	DupChecker_1.25.0.zip
macOS 10.13 (High Sierra)
Source Repository	git clone https://git.bioconductor.org/packages/DupChecker
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DupChecker
Package Short Url	https://bioconductor.org/packages/DupChecker/
Package Downloads Report	Download Stats