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REIDS (version 0.1.0)

Random Effects for the Identification of Differential Splicing

Description

Contains the REIDS model presented in Van Moerbeke et al (2017) for the detection of alternative splicing. The method is extended by incorporating junction information for the assessment of alternative splicing. The vignette introduces the model and shows an example work flow.

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Version

Install

install.packages('REIDS')

Monthly Downloads

4

Version

0.1.0

License

GPL-3

Maintainer

Marijke Van Moerbeke

Last Published

July 30th, 2018

Functions in REIDS (0.1.0)

CreateOutput

"CreateOutput"
ExampleFirmaOutput

Example data set for FIRMA
REIDSFunction

"REIDSFunction"
REIDS

Random Effects for the Identification of Differential Splicing.
TranscriptsPlot

"TranscriptsPlot "
reidsfunction_genebygene

"reidsfunction_genebygene"
node_coords

Node Coordinates
TC1500264

Example data set
iniREIDS

"iniREIDS"
TC12000010_transcript.clusters

Transcript Clusters
AnnotateGeneSymbol

"AnnotateGeneSymbol"
REIDSFunction_HPCVersion

"REIDS_HPCVersion"
ExonTesting

"ExonTesting"
ExpressionLevelPlot

"ExpressionLevelPlot"
REIDSmodel_intern

"REIDSmodel_intern"
REIDS_JunctionAssesment

REIDS_JunctionAssessment
JunInfo

JunInfo
min_max_margin

Minimum and Maximum Margin Limits
trim

"trim"
TC12000010

Example data set
REIDSJunctionAssessment_HPCVersion

REIDSJunctionAssessment_HPCVersion
TC12000010_ExonLevel

Exon level data
REMAP_SplitProbeSets

"REMAP_SplitProbeSets"
xynodes

X or Y coordinates of node locations
PivotTransformData

"PivotTransformation"
TC12000010_GeneLevel

Gene level data
TC12000010_REIDS_Output

REIDS Output
arcplot

Arc Diagram Plot
SpliceIndex

"SpliceIndex"
above_below

Above or Below
graph_info

Graph Information
arc_radius_locs

Arc Radius Locations
ASExons

"ASExons"
AnnotateGenes

"AnnotateGenes"
DataProcessing

DataProcessing
FIRMAScores

"FIRMAScores"
GetIntensities

"GetIntensities"
REIDS_Analysis

REIDS_Analysis
TC12000010_positions

Positions
REIDS_IsoformAssesment

REIDS_IsoformAssesment