XBSeq

Package: XBSeq
Type: Package
Title: Test for differential expression for RNA-seq data
Version: 1.2.2
Date: 2016-02-05
Author: Yuanhang Liu
Maintainer: Yuanhang Liu <liuy12@uthscsa.edu>
Description: We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.
License: GPL (>=3)
Imports: pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr,
Delaporte, magrittr
Depends: DESeq2, R (>= 3.2.0)
Suggests: knitr, DESeq, rmarkdown, BiocStyle, testthat
VignetteBuilder: knitr
biocViews: RNASeq, DifferentialExpression, Sequencing, Software,
ExperimentalDesign
URL: https://github.com/Liuy12/XBSeq
NeedsCompilation: no
Packaged: 2016-05-16 05:37:30 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'XBSeq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'XBSeq'
    finding HTML links ... done
    ExampleData                             html  
    MAplot                                  html  
    XBSeq-package                           html  
    XBSeq                                   html  
    XBSeqDataSet-class                      html  
    finding level-2 HTML links ... done

    XBSeqTest                               html  
    XBplot                                  html  
    conditions                              html  
    counts                                  html  
    dispEst                                 html  
    dispTable                               html  
    estimateRealCount                       html  
    estimateSCV                             html  
    fitInfo                                 html  
    getSignalVars                           html  
    plotSCVEsts                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (XBSeq)
Making 'packages.html' ... done