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roar (version 1.6.0)

Identify differential APA usage from RNA-seq alignments

Description

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

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Version

Version

1.6.0

License

GPL-3

Issues

2

Pull Requests

0

Stars

4

Forks

0

Maintainer

Elena Grassi

Last Published

February 15th, 2017

Functions in roar (1.6.0)

checkStep

Private/inner/helper method to check the order of the invoked analysis methods
combineFisherMethod

Private/inner/helper method to combine pvalues of independent test with the Fisher method
computeRoars

Computes m/M and roar values for this RoarDataset object
cores

Method to check how many cores are used by a roar analysis - right now not useful
getFisher

Private/inner/helper method to perform Fisher test
fpkmResults

Returns a dataframe with results of the analysis for a RoarDataset object
countPrePost

Counts reads falling over PRE/POST portions of the given transcripts
meanAcrossAssays

Private/inner/helper method to get average counts across samples
totalResults

Returns a dataframe with results of the analysis for a RoarDataset object
countResults

Returns a dataframe with results of the analysis for a RoarDataset object
computePvals

Computes pvalues (Fisher test) for this RoarDataset object
roar-package

Identify differential APA usage from RNA-seq alignments
RoarDataset-class

Class "RoarDataset"
computePairedPvals

Computes pvalues (Fisher test) for this RoarDataset object
RoarDatasetFromFiles

Creates a RoarDataset object