XBSeq: Test for differential expression for RNA-seq data

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
Date of publicationNone
MaintainerYuanhang Liu <liuy12@uthscsa.edu>
LicenseGPL (>=3)
Version1.4.0
https://github.com/Liuy12/XBSeq

View on Bioconductor

Functions

apaUsage Man page
Background Man page
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<- Man page
dispEst<-,XBSeqDataSet-method 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
ExampleData Man page
fitInfo Man page
fitInfo,XBSeqDataSet-method Man page
genelength Man page
getSignalVars Man page
MAplot Man page
Observed Man page
plotSCVEsts Man page
scvBiasCorrectionFits Man page
XBplot Man page
XBSeq Man page
XBSeqDataSet Man page
XBSeqDataSet-class Man page
XBSeq-package Man page
XBSeqTest Man page

Files

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

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