XBSeq

This package is for version 3.9 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: 3.9

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 (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("XBSeq")

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

Documentation

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

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

Details

biocViews DifferentialExpression, ExperimentalDesign, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL (>=3)
Depends DESeq2, R (>= 3.3)
Imports pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr, magrittr, roar
System Requirements
URL https://github.com/Liuy12/XBSeq
See More
Suggests knitr, DESeq, rmarkdown, BiocStyle, testthat
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Package Archives

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

Source Package XBSeq_1.16.0.tar.gz
Windows Binary XBSeq_1.16.0.zip
Mac OS X 10.11 (El Capitan) XBSeq_1.16.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/XBSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/XBSeq
Bioc Package Browser https://code.bioconductor.org/browse/XBSeq/
Package Short Url https://bioconductor.org/packages/XBSeq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive