roar: Identify differential APA usage from RNA-seq alignments

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Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.

Author
Elena Grassi
Date of publication
None
Maintainer
Elena Grassi <grassi.e@gmail.com>
License
GPL-3
Version
1.10.0
URLs

View on Bioconductor

Man pages

checkStep-method
Private/inner/helper method to check the order of the invoked...
combineFisherMethod-method
Private/inner/helper method to combine pvalues of independent...
computePairedPvals-method
Computes pvalues (Fisher test) on the read counts in this...
computePvals-method
Computes pvalues (Fisher test) on the read counts in this...
computeRoars-method
Computes m/M and roar values
cores-method
Method to check how many cores are used by a roar analysis -...
countPrePost-method
Counts reads falling over PRE/POST portions of the given...
countResults-method
Returns a dataframe with results of the analysis for a...
fpkmResults-method
Returns a dataframe with results of the analysis for a...
getFisher-method
Private/inner/helper method to perform Fisher test
meanAcrossAssays-method
Private/inner/helper method to get average counts across...
pvalueCorrectFilter-method
Returns a dataframe with results of the analysis for a...
pvalueFilter-method
Returns a dataframe with results of the analysis for a...
RoarDataset-class
Class '"RoarDataset"'
RoarDataset-constructor
Creates a 'RoarDataset' object
RoarDatasetFromFiles-constructor
Creates a 'RoarDataset' object
RoarDatasetMultipleAPA-class
Class '"RoarDatasetMultipleAPA"'
RoarDatasetMultipleAPA-constructor
Creates a 'RoarDatasetMultipleAPA' object
RoarDatasetMultipleAPAFromFiles-constructor
Creates a 'RoarDatasetMultipleAPA' object
roar-package
Identify differential APA usage from RNA-seq alignments
standardFilter-method
Returns a dataframe with results of the analysis for a...
totalResults-method
Returns a dataframe with results of the analysis for a...

Files in this package

roar/DESCRIPTION
roar/NAMESPACE
roar/R
roar/R/AllClasses.R
roar/R/AllGenerics.R
roar/R/Roar-utils.R
roar/R/RoarDataset-accessors.R
roar/R/RoarDatasetMultipleAPA-accessors.R
roar/build
roar/build/vignette.rds
roar/inst
roar/inst/NEWS
roar/inst/doc
roar/inst/doc/roar.R
roar/inst/doc/roar.Rnw
roar/inst/doc/roar.pdf
roar/inst/examples
roar/inst/examples/apa.gtf
roar/inst/examples/roarWrapper.R
roar/inst/examples/roarWrapper_chrBychr.R
roar/inst/examples/roarWrapper_multipleAPA.R
roar/inst/examples/roarWrapper_multipleAPA_bf.R
roar/inst/examples/roarWrapper_multipleAPA_chrBychr.R
roar/inst/examples/roarWrapper_paired_chrBychr.R
roar/man
roar/man/RoarDataset-class.Rd
roar/man/RoarDataset-constructor.Rd
roar/man/RoarDatasetFromFiles-constructor.Rd
roar/man/RoarDatasetMultipleAPA-class.Rd
roar/man/RoarDatasetMultipleAPA-constructor.Rd
roar/man/RoarDatasetMultipleAPAFromFiles-constructor.Rd
roar/man/checkStep-method.Rd
roar/man/combineFisherMethod-method.Rd
roar/man/computePairedPvals-method.Rd
roar/man/computePvals-method.Rd
roar/man/computeRoars-method.Rd
roar/man/cores-method.Rd
roar/man/countPrePost-method.Rd
roar/man/countResults-method.Rd
roar/man/fpkmResults-method.Rd
roar/man/getFisher-method.Rd
roar/man/meanAcrossAssays-method.Rd
roar/man/pvalueCorrectFilter-method.Rd
roar/man/pvalueFilter-method.Rd
roar/man/roar-package.Rd
roar/man/standardFilter-method.Rd
roar/man/totalResults-method.Rd
roar/tests
roar/tests/testthat
roar/tests/testthat.R
roar/tests/testthat/test_roar.R
roar/tests/testthat/test_roar_multipleAPA.R
roar/tests/testthat/test_roar_results.R
roar/vignettes
roar/vignettes/prepost.pdf
roar/vignettes/roar.Rnw
roar/vignettes/roar.bib