XBSeq: Test for differential expression for RNA-seq data

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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
Date of publication
None
Maintainer
Yuanhang Liu <liuy12@uthscsa.edu>
License
GPL (>=3)
Version
1.4.0
URLs

View on Bioconductor

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

Files in this package

XBSeq/DESCRIPTION
XBSeq/NAMESPACE
XBSeq/NEWS
XBSeq/R
XBSeq/R/class_and_slots.R
XBSeq/R/core_functions.R
XBSeq/R/methods.R
XBSeq/R/plots.R
XBSeq/R/welcome.R
XBSeq/README.md
XBSeq/data
XBSeq/data/ExampleData.rdata
XBSeq/data/scvBiasCorrectionFits.rda
XBSeq/inst
XBSeq/inst/doc
XBSeq/inst/scripts
XBSeq/inst/scripts/GEFRshift.pl
XBSeq/inst/scripts/exonFreeRegionShift.pl
XBSeq/man
XBSeq/man/ExampleData.Rd
XBSeq/man/MAplot.Rd
XBSeq/man/XBSeq-package.Rd
XBSeq/man/XBSeq.Rd
XBSeq/man/XBSeqDataSet-class.Rd
XBSeq/man/XBSeqTest.Rd
XBSeq/man/XBplot.Rd
XBSeq/man/apaUsage.Rd
XBSeq/man/conditions.Rd
XBSeq/man/counts.Rd
XBSeq/man/dispEst.Rd
XBSeq/man/dispTable.Rd
XBSeq/man/estimateRealCount.Rd
XBSeq/man/estimateSCV.Rd
XBSeq/man/fitInfo.Rd
XBSeq/man/getSignalVars.Rd
XBSeq/man/plotSCVEsts.Rd
XBSeq/tests
XBSeq/tests/testthat
XBSeq/tests/testthat.R
XBSeq/tests/testthat/test_1v1.R
XBSeq/tests/testthat/test_XBSeqDataSet.R
XBSeq/tests/testthat/test_XBSeqTest.R
XBSeq/tests/testthat/test_XBplot.R
XBSeq/tests/testthat/test_estimateRealCount.R
XBSeq/tests/testthat/test_estimateSCV.R
XBSeq/tests/testthat/test_estimateSizeFactors.R
XBSeq/vignettes
XBSeq/vignettes/XBSeq.Rmd