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

AuthorNing Leng, Christina Kendziorski
Date of publicationNone
MaintainerNing Leng <lengning1@gmail.com>
LicenseArtistic-2.0
Version1.14.0

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

Functions

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

Files

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

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