XBSeq

DOI: 10.18129/B9.bioc.XBSeq    

This package is for version 3.9 of Bioconductor; for the 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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	DifferentialExpression, ExperimentalDesign, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.16.0
In Bioconductor since	BioC 3.2 (R-3.2) (4 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
Links To Me
Build Report

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
Package Short Url	https://bioconductor.org/packages/XBSeq/
Package Downloads Report	Download Stats