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 |
BuildTree |
Hierachical Clustering based on EBSeq DE analysis |
CheckNg |
CheckNgStructure |
crit_fun |
Calculate the adjusted FDR threshold |
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 multiple condition study |
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 Predictive Distribution of being EE |
f1 |
f1(Input, AlphaIn, BetaIn, EmpiricalR, NumOfGroups, log) |
GeneEBresultGouldBart2 |
The EBSeq result of the empirical gene data ( Gould Lab data, bart2 ) |
GeneMat |
The simulated data for two condition gene DE analysis |
GeneMultiSimu |
Gene Level Simulation for multiple conditions |
GeneSimu |
Gene Level Simulation |
GeneSimuAt |
Gene Level Simulation with outliers |
GetData |
Read in RSEM output of Gould data |
GetMultiFC |
Calculate the Fold Changes for each pair of conditions |
GetMultiPP |
Generate the Posterior Probability of each transcript. |
GetNg |
Generate the Ng vector |
GetPatterns |
Generate all possible patterns in multiple condtion study |
GetPP |
Generate the Posterior Probability of each transcript. |
GetPPMat |
Generate the Posterior Probability of each transcript. |
GetR |
Calculate the R |
IsoEBresultGouldBart2 |
The EBSeq result of the empirical isoform data ( Gould Lab data, bart2 ) |
IsoList |
The simulated data for two condition isoform DE analysis |
IsoSimu |
Isoform level simulation |
IsoSimuAt |
Isoform level simulation with outliers |
Likefun |
Likelihood Function of the NB-Beta Model |
LikefunMulti |
Likelihood Function of the NB-Beta Model |
LogN |
The function to run EM (one round) using optim. |
LogNMulti |
The function to run EM (one round) using optim. |
MedianNorm |
Median Normalization |
MergeGene |
Plots of gene simulation result |
MergeIso |
Isoforms of gene simulation result |
MultiGeneMat |
The simulated data for multiple condition gene DE analysis |
PlotPattern |
Visualize the patterns |
PlotPostVsRealFC |
Plot Posterior FC vs FC |
PlotTree |
Plot the dendrograph of the hierachical cluster results from EBSeq |
PolyFitPlot |
Fit the mean-var relationship using polynomial regression |
PoolMatrix |
Generate the expression matrix from the output of GetData |
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 |
WithinDE |
Test each sample with the other ones |