XBSeq: Test for differential expression for RNA-seq data
Version 1.6.0

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.

AuthorYuanhang Liu
Bioconductor views DifferentialExpression ExperimentalDesign RNASeq Sequencing Software
Date of publicationNone
MaintainerYuanhang Liu <liuy12@uthscsa.edu>
LicenseGPL (>=3)
Version1.6.0
URL https://github.com/Liuy12/XBSeq
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("XBSeq")

Getting started

Package overview
README.md
Differential expression and apa usage analysis of count data using XBSeq package

Popular man pages

dispEst: Function to access the dispersion estimation for each gene
dispTable: Access the dispersion table information for a XBSeqDataSet...
estimateSCV: Estimate squared coefficient of variation for each gene
ExampleData: Example Datasets used in the manual pages as well as in...
fitInfo: Accessor function for the fitInfo objects in a XBSeqDataSet
plotSCVEsts: Plot estimated squared coefficient of variation
XBSeq: Express function to carry out XBSeq analysis
See all...

All man pages Function index File listing

Man pages

apaUsage: Testing differential alternative polyadenylation (apa) usage...
conditions: Accessor functions for the 'conditions' information in a...
counts: Accessor functions for the 'counts' information in a...
dispEst: Function to access the dispersion estimation for each gene
dispTable: Access the dispersion table information for a XBSeqDataSet...
estimateRealCount: Preliminary step to estimate the true signal based on...
estimateSCV: Estimate squared coefficient of variation for each gene
ExampleData: Example Datasets used in the manual pages as well as in...
fitInfo: Accessor function for the fitInfo objects in a XBSeqDataSet
getSignalVars: Estimate variance of the signal based on variance summation...
MAplot: Generate maplot after differential expression test
plotSCVEsts: Plot estimated squared coefficient of variation
XBplot: Examine the distribution of observed signal and background...
XBSeq: Express function to carry out XBSeq analysis
XBSeqDataSet-class: Class '"XBSeqDataSet"'
XBSeq-package: Differential expression analysis of RNA sequencing data by...
XBSeqTest: XBSeq test for differential expression

Functions

Background Man page
ExampleData Man page
Loglikhood Source code
Loglikhood_NB Source code
MAplot Man page Source code
Observed Man page
XBSeq Man page Source code
XBSeq-package Man page
XBSeqDataSet Man page Source code
XBSeqDataSet-class Man page
XBSeqTest Man page Source code
XBSeqTestForMatrices Source code
XBplot Man page Source code
adjustScv Source code
apaUsage Man page Source code
conditions Man page
conditions,XBSeqDataSet-method Man page
conditions<-,XBSeqDataSet-method Man page
counts Man page
counts,XBSeqDataSet-method Man page
dispEst Man page
dispEst,XBSeqDataSet-method Man page
dispEst<- Man page
dispEst<-,XBSeqDataSet-method Man page
dispTable Man page
dispTable,XBSeqDataSet-method Man page
estimateRealCount Man page
estimateRealCount,XBSeqDataSet-method Man page
estimateSCV Man page
estimateSCV,XBSeqDataSet-method Man page
estimation_param_PoissonNB_MLE Source code
estimation_param_PoissonNB_MLE_NB Source code
exactTestBetaApprox Source code
fitInfo Man page
fitInfo,XBSeqDataSet-method Man page
genelength Man page
getCountParams Source code
getCountParamsPooled Source code
getSCV Source code
getSignalVars Man page Source code
insertRow Source code
onAttach Source code
parametricscvFit Source code
plotSCVEsts Man page Source code
predict_helper Source code
prepareScvBiasCorrectionFits Source code
scvBiasCorrectionFits Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/class_and_slots.R
R/core_functions.R
R/methods.R
R/plots.R
R/welcome.R
README.md
build
build/vignette.rds
data
data/ExampleData.rdata
data/scvBiasCorrectionFits.rda
inst
inst/doc
inst/doc/XBSeq.R
inst/doc/XBSeq.Rmd
inst/doc/XBSeq.html
inst/scripts
inst/scripts/GEFRshift.pl
inst/scripts/exonFreeRegionShift.pl
man
man/ExampleData.Rd
man/MAplot.Rd
man/XBSeq-package.Rd
man/XBSeq.Rd
man/XBSeqDataSet-class.Rd
man/XBSeqTest.Rd
man/XBplot.Rd
man/apaUsage.Rd
man/conditions.Rd
man/counts.Rd
man/dispEst.Rd
man/dispTable.Rd
man/estimateRealCount.Rd
man/estimateSCV.Rd
man/fitInfo.Rd
man/getSignalVars.Rd
man/plotSCVEsts.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_1v1.R
tests/testthat/test_XBSeqDataSet.R
tests/testthat/test_XBSeqTest.R
tests/testthat/test_XBplot.R
tests/testthat/test_estimateRealCount.R
tests/testthat/test_estimateSCV.R
tests/testthat/test_estimateSizeFactors.R
vignettes
vignettes/XBSeq.Rmd
XBSeq documentation built on May 20, 2017, 9:39 p.m.

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