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

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

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