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 |
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 |
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 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 |