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| baySeq-package | Empirical Bayesian analysis of patterns of differential expression in count data. |
| baySeq | Empirical Bayesian analysis of patterns of differential expression in count data. |
| baySeq-class | baySeq - classes |
| baySeq-classes | baySeq - classes |
| countData | baySeq - classes |
| countData-class | baySeq - classes |
| countDataPosterior | baySeq - classes |
| countDataPosterior-class | baySeq - classes |
| dim,countData-method | baySeq - classes |
| dim,countDataPosterior-method | baySeq - classes |
| factCount | Simulated data for testing the baySeq package methods; simulated counts from a factorial design differential expression analysis |
| factlibsizes | Simulated data for testing the baySeq package methods; simulated library sizes from a pairwise differential expression analysis |
| getLikelihoods | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getLikelihoods.Dirichlet | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getLikelihoods.NBboot | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getLikelihoods.Pois | Finds posterior likelihoods for each count as belonging to some hypothesis. |
| getPosteriors | An internal function in the baySeq package for calculating posterior likelihoods given likelihoods of the data. |
| getPriors | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.Dirichlet | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.NB | Estimates prior parameters for the underlying distributions of 'count' data. |
| getPriors.Pois | Estimates prior parameters for the underlying distributions of 'count' data. |
| getTPs | Gets the number of true positives in the top n counts selected by ranked posterior likelihoods |
| libsizes | Simulated data for testing the baySeq package methods; simulated library sizes from a pairwise differential expression analysis |
| logsum | An internal function for the baySeq package that calculates the log of the sum of the exponential of two variables |
| PDgivenr | Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution. |
| PDgivenr.Dirichlet | Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution. |
| PDgivenr.NBIndie | Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution. |
| PDgivenr.Pois | Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution. |
| PDgivenr.PoisIndie | Functions for estimating the likelihood of the data given an equivalence relation for some assumption on the distribution. |
| show,countData-method | baySeq - classes |
| show,countDataPosterior-method | baySeq - classes |
| simCount | Simulated data for testing the baySeq package methods; simulated counts from a pairwise differential expression analysis |
| topCounts | Get the top counts corresponding to some group from a 'countDataPosterior' object |
| [,countData-method | baySeq - classes |
| [,countDataPosterior-method | baySeq - classes |