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

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

Author
Ning Leng, Christina Kendziorski
Date of publication
None
Maintainer
Ning Leng <lengning1@gmail.com>
License
Artistic-2.0
Version
1.14.0

View on Bioconductor

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

Files in this package

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