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
|
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see XBSeq.
Test for differential expression for RNA-seq data
Bioconductor version: 3.2
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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("XBSeq")
| HTML | Differential expression analysis of count data using XBSeq package | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, ExperimentalDesign, RNASeq, Sequencing, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 3.2 (R-3.2) (0.5 years) |
| License | GPL (>=3) |
| Depends | DESeq2, R (>= 3.2.0) |
| Imports | pracma, matrixStats, locfit, ggplot2, methods, Biobase, dplyr, Delaporte, magrittr |
| 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
Follow Installation instructions to use this package in your R session.
| Package Source | XBSeq_1.0.2.tar.gz |
| Windows Binary | XBSeq_1.0.2.zip |
| Mac OS X 10.6 (Snow Leopard) | XBSeq_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | XBSeq_1.0.2.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/XBSeq/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/XBSeq/ |
| Package Downloads Report | Download Stats |
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