To install this package, start R and enter:

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

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

XBSeq

   

Test for differential expression for RNA-seq data

Bioconductor version: 3.2

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.

Author: Yuanhang Liu

Maintainer: Yuanhang Liu <liuy12 at uthscsa.edu>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("XBSeq")

 

HTML Differential expression analysis of count data using XBSeq package
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, ExperimentalDesign, RNASeq, Sequencing, Software
Version 1.0.2
In Bioconductor since BioC 3.2 (R-3.2) (0.5 years)
License GPL (>=3)
Depends DESeq2, R (>= 3.2.0)
Imports pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr, Delaporte, magrittr
LinkingTo
Suggests knitr, DESeq, rmarkdown, BiocStyle, testthat
SystemRequirements
Enhances
URL https://github.com/Liuy12/XBSeq
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source XBSeq_1.0.2.tar.gz
Windows Binary XBSeq_1.0.2.zip
Mac OS X 10.6 (Snow Leopard) XBSeq_1.0.0.tgz
Mac OS X 10.9 (Mavericks) XBSeq_1.0.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/XBSeq/tree/release-3.2
Package Short Url http://bioconductor.org/packages/XBSeq/
Package Downloads Report Download Stats

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