To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("NADfinder")

In most cases, you don't need to download the package archive at all.

NADfinder

 

   

Call wide peaks for sequencing data

Bioconductor version: Release (3.5)

Call peaks for two samples: target and control. It will count the reads for tiles of the genome and then convert it to ratios. The ratios will be corrected and smoothed. The z-scores is calculated for each counting windows over the background. The peaks will be detected based on z-scores.

Author: Jianhong Ou, Jun Yu, Paul Kaufman, Lihua Julie Zhu

Maintainer: Jianhong Ou <jianhong.ou at umassmed.edu>, Lihua Julie Zhu <julie.zhu at umassmed.edu>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("NADfinder")

Documentation

HTML R Script NADfinder Vignette
PDF   Reference Manual

Details

biocViews DNASeq, GeneRegulation, PeakDetection, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.5 (R-3.4) (< 6 months)
License GPL (>= 2)
Depends R (>= 3.4), BiocGenerics, IRanges, GenomicRanges, S4Vectors
Imports graphics, methods, baseline, signal, GenomicAlignments, GenomeInfoDb, rtracklayer, SummarizedExperiment, limma, trackViewer, stats, utils
LinkingTo
Suggests RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat
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 NADfinder_1.0.0.tar.gz
Windows Binary NADfinder_1.0.0.zip
Mac OS X 10.11 (El Capitan) NADfinder_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/NADfinder/tree/release-3.5
Package Short Url http://bioconductor.org/packages/NADfinder/
Package Downloads Report Download Stats

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