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("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 | ||
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 |