DOI: 10.18129/B9.bioc.XBSeq    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see XBSeq.

Test for differential expression for RNA-seq data

Bioconductor version: 3.13

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")):


To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


PDF   Reference Manual


biocViews DifferentialExpression, ExperimentalDesign, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.24.0
In Bioconductor since BioC 3.2 (R-3.2) (6 years)
License GPL (>=3)
Depends DESeq2, R (>= 3.3)
Imports pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr, magrittr, roar
Suggests knitr, DESeq, rmarkdown, BiocStyle, testthat
URL https://github.com/Liuy12/XBSeq
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/XBSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/XBSeq
Package Short Url https://bioconductor.org/packages/XBSeq/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: