DupChecker

This package is for version 3.9 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: 3.9

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>

Citation (from within R, enter citation("DupChecker")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("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")
Validate genomic data with "DupChecker" package PDF R Script
Reference Manual PDF

Details

biocViews Preprocessing, Software
Version 1.22.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL (>= 2)
Depends
Imports tools, R.utils, RCurl
System Requirements
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Package Archives

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

Source Package DupChecker_1.22.0.tar.gz
Windows Binary DupChecker_1.22.0.zip
Mac OS X 10.11 (El Capitan) DupChecker_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DupChecker
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DupChecker
Bioc Package Browser https://code.bioconductor.org/browse/DupChecker/
Package Short Url https://bioconductor.org/packages/DupChecker/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive