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

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

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