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.

AuthorElena Grassi
Date of publicationNone
MaintainerElena Grassi <grassi.e@gmail.com>
LicenseGPL-3
Version1.10.0
https://github.com/vodkatad/roar/

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...

Functions

checkStep Man page
combineFisherMethod Man page
computePairedPvals Man page
computePairedPvals, RoarDataset Man page
computePairedPvals, RoarDatasetMultipleAPA Man page
computePairedPvals,RoarDatasetMultipleAPA,numeric,numeric-method Man page
computePairedPvals,RoarDataset,numeric,numeric-method Man page
computePvals Man page
computePvals, RoarDataset Man page
computePvals,RoarDataset-method Man page
computePvals, RoarDatasetMultipleAPA Man page
computePvals,RoarDatasetMultipleAPA-method Man page
computeRoars Man page
computeRoars,RoarDataset-method Man page
computeRoars,RoarDatasetMultipleAPA-method Man page
computeRoars, RoarDatasetMultipleAPA, numeric, numeric Man page
computeRoars, RoarDataset, numeric, numeric Man page
cores Man page
cores,RoarDataset-method Man page
cores,RoarDatasetMultipleAPA-method Man page
countPrePost Man page
countPrePost,RoarDataset,logical Man page
countPrePost,RoarDataset,logical-method Man page
countPrePost,RoarDataset-method Man page
countPrePost,RoarDatasetMultipleAPA Man page
countPrePost,RoarDatasetMultipleAPA,logical-method Man page
countPrePost,RoarDatasetMultipleAPA-method Man page
countResults Man page
countResults, RoarDataset Man page
countResults,RoarDataset-method Man page
countResults, RoarDatasetMultipleAPA Man page
countResults,RoarDatasetMultipleAPA-method Man page
fpkmResults Man page
fpkmResults, RoarDataset Man page
fpkmResults,RoarDataset-method Man page
fpkmResults, RoarDatasetMultipleAPA Man page
fpkmResults,RoarDatasetMultipleAPA-method Man page
getFisher Man page
meanAcrossAssays Man page
pvalueCorrectFilter Man page
pvalueCorrectFilter, RoarDataset Man page
pvalueCorrectFilter, RoarDatasetMultipleAPA Man page
pvalueCorrectFilter,RoarDatasetMultipleAPA,numeric,numeric,chara Man page
pvalueCorrectFilter,RoarDataset,numeric,numeric,character-method Man page
pvalueFilter Man page
pvalueFilter, RoarDataset Man page
pvalueFilter, RoarDatasetMultipleAPA Man page
pvalueFilter,RoarDatasetMultipleAPA,numeric,numeric-method Man page
pvalueFilter,RoarDataset,numeric,numeric-method Man page
roar Man page
RoarDataset Man page
RoarDataset-class Man page
RoarDatasetFromFiles Man page
RoarDatasetMultipleAPA Man page
RoarDatasetMultipleAPA-class Man page
RoarDatasetMultipleAPAFromFiles Man page
roar-package Man page
standardFilter Man page
standardFilter, RoarDataset Man page
standardFilter, RoarDatasetMultipleAPA Man page
standardFilter,RoarDatasetMultipleAPA,numeric-method Man page
standardFilter,RoarDataset,numeric-method Man page
totalResults Man page
totalResults, RoarDataset Man page
totalResults,RoarDataset-method Man page
totalResults, RoarDatasetMultipleAPA Man page
totalResults,RoarDatasetMultipleAPA-method Man page

Files

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

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