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

DOI: 10.18129/B9.bioc.XBSeq    

This is the development version of XBSeq; for the stable release version, see XBSeq.

Test for differential expression for RNA-seq data

Bioconductor version: Development (3.7)

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

HTML R Script Differential expression and apa usage analysis of count data using XBSeq package
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, ExperimentalDesign, RNASeq, Sequencing, Software
Version 1.9.0
In Bioconductor since BioC 3.2 (R-3.2) (2 years)
License GPL (>=3)
Depends DESeq2, R (>= 3.3)
Imports pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr, magrittr, roar
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

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Source Package XBSeq_1.9.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) XBSeq_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/XBSeq
Package Short Url http://bioconductor.org/packages/XBSeq/
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