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

## Documentation for package ‘EBSeq’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

EBSeq_NingLeng-package | EBSeq: RNA-Seq Differential Expression Analysis on both gene and isoform level
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 q's from the fitted beta distribution.
EBMultiTest | Using EM algorithm to calculate the posterior probabilities of interested patterns in a multiple condition study
EBSeqTest | EBSeq core
EBSeq_NingLeng | EBSeq: RNA-Seq Differential Expression Analysis on both gene and isoform level
EBTest | Using EM algorithm to calculate the posterior probabilities of being DE
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 Two-condition Test
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
GetPPMat | Posterior Probability of Transcripts
GetSelectedPatterns | Get selected patterns in a multiple condition study
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 Condition Test
LogN | The function to run EM (one round) algorithm for the NB-beta model.
LogNMulti | EM algorithm for the NB-beta model in the multiple condition test
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 across conditions
QQP | The Quantile-Quantile Plot to compare the empirical q's and simulated q's from fitted beta distribution
QuantileNorm | Quantile Normalization
RankNorm | Rank Normalization