- Home
- Bioconductor 3.0
- Software Packages
- DupChecker
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DupChecker")
In most cases, you don't need to download the package archive at all.
DupChecker
a package for checking high-throughput genomic data redundancy in meta-analysis
Bioconductor version: 3.0
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 and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DupChecker")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DupChecker")
| R Script | Validate genomic data with "DupChecker" package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Preprocessing, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | GPL (>= 2) |
| Depends | |
| Imports | tools, R.utils, RCurl |
| LinkingTo | |
| Suggests | knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DupChecker_1.4.0.tar.gz |
| Windows Binary | DupChecker_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | DupChecker_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | DupChecker_1.4.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
