EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data
Version 1.16.0

Differential Expression analysis at both gene and isoform level using RNA-seq data

AuthorNing Leng, Christina Kendziorski
Bioconductor views DifferentialExpression MultipleComparison RNASeq Sequencing StatisticalMethod
Date of publicationNone
MaintainerNing Leng <lengning1@gmail.com>
LicenseArtistic-2.0
Version1.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EBSeq")

Getting started

README.md

Popular man pages

EBMultiTest: Using EM algorithm to calculate the posterior probabilities...
EBTest: Using EM algorithm to calculate the posterior probabilities...
GetMultiFC: Calculate the Fold Changes for Multiple Conditions
GetNg: Ng Vector
MedianNorm: Median Normalization
PlotPostVsRawFC: Plot Posterior FC vs FC
PostFC: Calculate the posterior fold change for each transcript...
See all...

All man pages Function index File listing

Man pages

beta.mom: Fit the beta distribution by method of moments
crit_fun: Calculate the soft threshold for a target FDR
DenNHist: Density plot to compare the empirical q's and the simulated...
EBMultiTest: Using EM algorithm to calculate the posterior probabilities...
EBSeq_NingLeng-package: EBSeq: RNA-Seq Differential Expression Analysis on both gene...
EBTest: Using EM algorithm to calculate the posterior probabilities...
f0: The Prior Predictive Distribution of being EE
f1: The Prior Predictive Distribution of being DE
GeneMat: The simulated data for two condition gene DE analysis
GetDEResults: Obtain Differential Expression Analysis Results in a...
GetMultiFC: Calculate the Fold Changes for Multiple Conditions
GetMultiPP: Posterior Probability of Each Transcript
GetNg: Ng Vector
GetNormalizedMat: Calculate normalized expression matrix
GetPatterns: Generate all possible patterns in a multiple condition study
GetPP: Generate the Posterior Probability of each transcript.
GetPPMat: Posterior Probability of Transcripts
IsoList: The simulated data for two condition isoform DE analysis
IsoMultiList: The simulated data for multiple condition isoform DE analysis
Likefun: Likelihood Function of the NB-Beta Model
LikefunMulti: Likelihood Function of the NB-Beta Model In Multiple...
LogN: The function to run EM (one round) algorithm for the NB-beta...
LogNMulti: EM algorithm for the NB-beta model in the multiple condition...
MedianNorm: Median Normalization
MultiGeneMat: The simulated data for multiple condition gene DE analysis
PlotPattern: Visualize the patterns
PlotPostVsRawFC: Plot Posterior FC vs FC
PolyFitPlot: Fit the mean-var relationship using polynomial regression
PostFC: Calculate the posterior fold change for each transcript...
QQP: The Quantile-Quantile Plot to compare the empirical q's and...
QuantileNorm: Quantile Normalization
RankNorm: Rank Normalization

Functions

DenNHist Man page Source code
EBMultiTest Man page Source code
EBSeq_NingLeng Man page
EBSeq_NingLeng-package Man page
EBTest Man page Source code
GeneMat Man page
GetDEResults Man page Source code
GetMultiFC Man page Source code
GetMultiPP Man page Source code
GetNg Man page Source code
GetNormalizedMat Man page Source code
GetPP Man page Source code
GetPPMat Man page Source code
GetPatterns Man page Source code
IsoList Man page
IsoMultiList Man page
Likefun Man page Source code
LikefunMulti Man page Source code
LogN Man page Source code
LogNMulti Man page Source code
MedianNorm Man page Source code
MultiGeneMat Man page
PlotPattern Man page Source code
PlotPostVsRawFC Man page Source code
PolyFitPlot Man page Source code
PostFC Man page Source code
QQP Man page Source code
QuantileNorm Man page Source code
RankNorm Man page Source code
beta.mom Man page Source code
crit_fun Man page Source code
f0 Man page Source code
f1 Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/DenNHist.R
R/EBMultiTest.R
R/EBTest.R
R/GetDEResults.R
R/GetMultiFC.R
R/GetMultiPP.R
R/GetNg.R
R/GetNormalizedMat.R
R/GetPP.R
R/GetPPMat.R
R/GetPatterns.R
R/Likefun.R
R/LikefunMulti.R
R/LogN.R
R/LogNMulti.R
R/MedianNorm.R
R/PlotPattern.R
R/PlotPostVsRawFC.R
R/PolyFitPlot.R
R/PostFC.R
R/QQP.R
R/QuantileNorm.R
R/RankNorm.R
R/beta.mom.R
R/crit_fun.R
R/f0.R
R/f1.R
README.md
build
build/vignette.rds
data
data/GeneMat.rda
data/IsoList.rda
data/IsoMultiList.rda
data/MultiGeneMat.rda
demo
demo/00Index
demo/EBSeq.R
inst
inst/doc
inst/doc/EBSeq_Vignette.R
inst/doc/EBSeq_Vignette.Rnw
inst/doc/EBSeq_Vignette.pdf
man
man/DenNHist.Rd
man/EBMultiTest.Rd
man/EBSeq_NingLeng-package.Rd
man/EBTest.Rd
man/GeneMat.Rd
man/GetDEResults.Rd
man/GetMultiFC.Rd
man/GetMultiPP.Rd
man/GetNg.Rd
man/GetNormalizedMat.Rd
man/GetPP.Rd
man/GetPPMat.Rd
man/GetPatterns.Rd
man/IsoList.Rd
man/IsoMultiList.Rd
man/Likefun.Rd
man/LikefunMulti.Rd
man/LogN.Rd
man/LogNMulti.Rd
man/MedianNorm.Rd
man/MultiGeneMat.Rd
man/PlotPattern.Rd
man/PlotPostVsRawFC.Rd
man/PolyFitPlot.Rd
man/PostFC.Rd
man/QQP.Rd
man/QuantileNorm.Rd
man/RankNorm.Rd
man/beta.mom.Rd
man/crit_fun.Rd
man/f0.Rd
man/f1.Rd
vignettes
vignettes/EBSeq_Vignette.Rnw
vignettes/PlotExample.png
vignettes/lengetal.bib
EBSeq documentation built on May 20, 2017, 10:08 p.m.