Man pages for EBSeq
An R package for gene and isoform differential expression analysis of RNA-seq data
| 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 |
