Package: roar 1.41.0
Elena Grassi
roar: Identify differential APA usage from RNA-seq alignments
Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.
Authors:
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roar/json (API)
NEWS
| # Install 'roar' in R: |
| install.packages('roar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/vodkatad/roar/issues
On BioConductor:roar-1.41.0(bioc 3.20)roar-1.40.0(bioc 3.19)
Last updated 2 months agofrom:2aafb4dc2d
Exports:computePairedPvalscomputePvalscomputeRoarscountPrePostcountResultsfpkmResultspvalueCorrectFilterpvalueFilterRoarDatasetRoarDatasetFromFilesRoarDatasetMultipleAPARoarDatasetMultipleAPAFromFilesstandardFiltertotalResults
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Identify differential APA usage from RNA-seq alignments | roar-package roar |
| Private/inner/helper method to check the order of the invoked analysis methods | checkStep |
| Private/inner/helper method to combine pvalues of independent test with the Fisher method | combineFisherMethod |
| Computes pvalues (Fisher test) on the read counts in this roar analysis | computePairedPvals computePairedPvals, RoarDataset computePairedPvals, RoarDatasetMultipleAPA |
| Computes pvalues (Fisher test) on the read counts in this roar analysis | computePvals computePvals, RoarDataset computePvals, RoarDatasetMultipleAPA |
| Computes m/M and roar values | computeRoars computeRoars, RoarDataset, numeric, numeric computeRoars, RoarDatasetMultipleAPA, numeric, numeric |
| Method to check how many cores are used by a roar analysis - right now not useful | cores |
| Counts reads falling over PRE/POST portions of the given transcripts | countPrePost countPrePost,RoarDataset,logical countPrePost,RoarDatasetMultipleAPA |
| Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object | countResults countResults, RoarDataset countResults, RoarDatasetMultipleAPA |
| Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object | fpkmResults fpkmResults, RoarDataset fpkmResults, RoarDatasetMultipleAPA |
| Private/inner/helper method to perform Fisher test | getFisher |
| Private/inner/helper method to get average counts across samples | meanAcrossAssays |
| Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object | pvalueCorrectFilter pvalueCorrectFilter, RoarDataset pvalueCorrectFilter, RoarDatasetMultipleAPA |
| Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object | pvalueFilter pvalueFilter, RoarDataset pvalueFilter, RoarDatasetMultipleAPA |
| Creates a 'RoarDataset' object | RoarDataset |
| Class '"RoarDataset"' | computePairedPvals,RoarDataset,numeric,numeric-method computePvals,RoarDataset-method computeRoars,RoarDataset-method cores,RoarDataset-method countPrePost,RoarDataset,logical-method countPrePost,RoarDataset-method countResults,RoarDataset-method fpkmResults,RoarDataset-method pvalueCorrectFilter,RoarDataset,numeric,numeric,character-method pvalueFilter,RoarDataset,numeric,numeric-method RoarDataset-class standardFilter,RoarDataset,numeric-method totalResults,RoarDataset-method |
| Creates a 'RoarDataset' object | RoarDatasetFromFiles |
| Creates a 'RoarDatasetMultipleAPA' object | RoarDatasetMultipleAPA |
| Class '"RoarDatasetMultipleAPA"' | computePairedPvals,RoarDatasetMultipleAPA,numeric,numeric-method computePvals,RoarDatasetMultipleAPA-method computeRoars,RoarDatasetMultipleAPA-method cores,RoarDatasetMultipleAPA-method countPrePost,RoarDatasetMultipleAPA,logical-method countPrePost,RoarDatasetMultipleAPA-method countResults,RoarDatasetMultipleAPA-method fpkmResults,RoarDatasetMultipleAPA-method pvalueCorrectFilter,RoarDatasetMultipleAPA,numeric,numeric,character-method pvalueFilter,RoarDatasetMultipleAPA,numeric,numeric-method RoarDatasetMultipleAPA-class standardFilter,RoarDatasetMultipleAPA,numeric-method totalResults,RoarDatasetMultipleAPA-method |
| Creates a 'RoarDatasetMultipleAPA' object | RoarDatasetMultipleAPAFromFiles |
| Returns a dataframe with results of the analysis for a 'RoarDataset' object or a 'RoarDatasetMultipleAPA' object | standardFilter standardFilter, RoarDataset standardFilter, RoarDatasetMultipleAPA |
| Returns a dataframe with results of the analysis for a 'RoarDataset' or a 'RoarDatasetMultipleAPA' object | totalResults totalResults, RoarDataset totalResults, RoarDatasetMultipleAPA |
