casper: Characterization of Alternative Splicing based on Paired-End Reads

Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("casper")
AuthorDavid Rossell, Camille Stephan-Otto, Manuel Kroiss, Miranda Stobbe, Victor Pena
Bioconductor views DifferentialExpression GeneExpression RNASeq Sequencing Transcription
Date of publicationNone
MaintainerDavid Rossell <rosselldavid@gmail.com>
LicenseGPL (>=2)
Version2.8.0

View on Bioconductor

Man pages

annotatedGenome-class: Class "annotatedGenome"

asymmetryCheck: Plot asymmetry coefficients for the observed data and compare...

calcDenovo: Estimate expression of gene splicing variants de novo.

calcExp: Estimate expression of a known set of gene splicing variants.

denovoExpr: Estimate expression for de novo splicing variants.

denovoGeneExpr-class: Class "denovoGenomeExpr"

denovoGenomeExpr-class: Class "denovoGeneExpr"

distrsGSE37704: Estimated read start and insert size distributions from MiSeq...

genePlot: Plot exon structure for each transcript of a given gene.

getDistrs: Compute fragment start and fragment length distributions

getIsland: getIsland returns the island id associated to a given entrez...

getNreads: Get total number of paths in each island from a pathCounts...

getReads: getReads returns the reads stored in a 'procBam' object.

getRoc: Operating characteristics of differential expression analysis

hg19DB: Subset of human genome (UCSC hg19 version)

K562.r1l1: Toy RNA-seq data from RGASP project.

mergeBatches: Merge two ExpressionSet objects by doing quantile...

mergeExp: Merge splicing variant expression from multiple samples

modelPrior: Set prior distribution on expressed splicing variants.

modelPriorAS-class: Class "modelPriorAS"

pathCounts: Compute exon path counts

pathCounts-class: Class "pathCounts"

plotExpr: Plot inferred gene structure and expression.

plot-methods: Plot estimated read start and fragment length distributions.

plotPriorAS: Plot prior distribution on set of expressed variants (i.e....

probNonEquiv: 'probNonEquiv' performs a Bayesian hypothesis test for...

procBam: Process BAM object

procBam-class: Class "procBam"

procGenome: Create an annotatedGenome object that stores information...

qqnormGenomeWide: Genome-wide qq-normal and qq-gamma plots

quantileNorm: Apply quantile normalization

relexprByGene: Compute relative expressions within each gene

rmShortInserts: Remove reads with short insert sizes from imported BAM files.

simMAE: Simulate Mean Absolute Error (MAE) in estimating isoform...

simMAEcheck: Model checking for One Sample Problems.

simMultSamples: Simulate paired end reads for multiple future samples based...

simReads: Function to simulate paired end reads following given read...

simulatedSamples-class: Class "simulatedSamples"

splitGenomeByLength: Split an annotatedGenome object into subsets according to...

subsetGenome: subsetGenome subsets an object of class annotatedGenome for a...

transcripts: Extracts transcript information (exon start and ends) from an...

txLength-methods: ~~ Methods for Function 'txLength' in Package 'casper' ~~

wrapDenovo: Run all necessary steps to get expression estimates from...

wrapKnown: Run all necessary steps to get expression estimates from...

Functions

annotatedGenome Man page
annotatedGenome-class Man page
as.list,denovoGenomeExpr-method Man page
asymmetryCheck Man page
asymmetryCheck,data.frame-method Man page
asymmetryCheck,ExpressionSet-method Man page
asymmetryCheck,matrix-method Man page
calcDenovo Man page
calcExp Man page
casperDesign Man page
coef,modelPriorAS,ANY,ANY,ANY-method Man page
coef,modelPriorAS-method Man page
coef,simulatedSamples-method Man page
createDenovoGenome Man page
denovoExpr Man page
[,denovoGeneExpr,ANY,ANY,ANY-method Man page
[[,denovoGeneExpr,ANY,ANY,ANY-method Man page
[[,denovoGeneExpr,ANY,ANY-method Man page
denovoGeneExpr-class Man page
[,denovoGenomeExpr,ANY,ANY,ANY-method Man page
[[,denovoGenomeExpr,ANY,ANY-method Man page
denovoGenomeExpr-class Man page
[[,denovoGenomeExpr-method Man page
distrsGSE37704 Man page
exprs,simulatedSamples-method Man page
genePlot Man page
genePlot,CompressedIRangesList,ANY,ANY,ANY,ANY-method Man page
genePlot,GRanges,ANY,ANY,ANY,ANY-method Man page
genePlot,GRangesList,ANY,ANY,ANY,ANY-method Man page
genePlot,IRanges,ANY,ANY,ANY,ANY-method Man page
genePlot,IRangesList,ANY,ANY,ANY,ANY-method Man page
genePlot-methods Man page
genePlot,missing,character,annotatedGenome,GRanges,ExpressionSet Man page
genePlot,missing,character,annotatedGenome,missing,missing-metho Man page
genePlot,missing,character,annotatedGenome,procBam,ExpressionSet Man page
genePlot,missing,character,annotatedGenome,procBam,missing-metho Man page
getChr Man page
getChr,character,missing,missing,annotatedGenome-method Man page
getChr-method Man page
getChr,missing,character,missing,annotatedGenome-method Man page
getChr,missing,missing,character,annotatedGenome-method Man page
getChr,missing,missing,missing,annotatedGenome-method Man page
getDistrs Man page
getIsland Man page
getIsland,character,missing,annotatedGenome-method Man page
getIsland,missing,character,annotatedGenome-method Man page
getNreads Man page
getNreads,pathCounts-method Man page
getReads Man page
getReads,procBam-method Man page
getRoc Man page
getRoc,logical,logical-method Man page
getRoc,matrix,matrix-method Man page
getRoc,numeric,numeric-method Man page
hg19DB Man page
K562.r1l1 Man page
lines Man page
lines,readDistrs-method Man page
matchTranscripts Man page
mergeBatches Man page
mergeBatches,ExpressionSet,ExpressionSet-method Man page
mergeBatches,ExpressionSet,simulatedSamples-method Man page
mergeExp Man page
modelPrior Man page
[,modelPriorAS,ANY,ANY,ANY-method Man page
modelPriorAS-class Man page
names,denovoGenomeExpr-method Man page
pathCounts Man page
pathCounts-class Man page
pathCounts,list-method Man page
pathCounts-method Man page
pathCounts,procBam-method Man page
plot Man page
plotExpr Man page
plotExpr,denovoGeneExpr-method Man page
plotExpr-methods Man page
plotPriorAS Man page
plotPriorAS-methods Man page
plotPriorAS,modelPriorAS-method Man page
plot,readDistrs,ANY-method Man page
plot,readDistrsList,ANY-method Man page
posprob Man page
posprob,denovoGeneExpr-method Man page
probNonEquiv Man page
probNonEquiv,ExpressionSet-method Man page
probNonEquiv,list-method Man page
procBam Man page
procBam,ANY-method Man page
procBam-class Man page
procBam,list,logical,integer,logical,character-method Man page
procBam,list,logical,integer,logical,missing-method Man page
procBam,list,logical,integer,missing,missing-method Man page
procBam,list,logical,missing,logical,missing-method Man page
procBam,list,logical,missing,missing,missing-method Man page
procBam,list,missing,integer,logical,missing-method Man page
procBam,list,missing,integer,missing,missing-method Man page
procBam,list,missing,missing,logical,missing-method Man page
procBam,list,missing,missing,missing,missing-method Man page
procBam,list,missing,numeric,missing,missing-method Man page
procBam-method Man page
procGenome Man page
procGenome,GRanges,ANY-method Man page
procGenome,GRanges-method Man page
procGenome,TxDb,ANY-method Man page
procGenome,TxDb-method Man page
pvalTreat Man page
pvalTreat,ExpressionSet-method Man page
pvalTreat,list-method Man page
qqgammaGenomeWide Man page
qqgammaGenomeWide,data.frame-method Man page
qqgammaGenomeWide,ExpressionSet-method Man page
qqgammaGenomeWide,matrix-method Man page
qqnormGenomeWide Man page
qqnormGenomeWide,data.frame-method Man page
qqnormGenomeWide,ExpressionSet-method Man page
qqnormGenomeWide,matrix-method Man page
quantileNorm Man page
quantileNorm,ExpressionSet-method Man page
quantileNorm,matrix-method Man page
relexprByGene Man page
rmShortInserts Man page
show,annotatedGenome-method Man page
show,denovoGeneExpr-method Man page
show,denovoGenomeExpr-method Man page
show,modelPriorAS-method Man page
show,pathCounts-method Man page
show,procBam-method Man page
show,simulatedSamples-method Man page
simMAE Man page
simMAEcheck Man page
simMultSamples Man page
simReads Man page
[,simulatedSamples,ANY,ANY,ANY-method Man page
simulatedSamples-class Man page
[,simulatedSamples,missing,index,missing-method Man page
splitGenomeByLength Man page
subsetGenome Man page
subsetGenome,character,missing,annotatedGenome-method Man page
subsetGenome-methods Man page
subsetGenome,missing,character,annotatedGenome-method Man page
transcripts Man page
transcripts,annotatedGenome,character,missing-method Man page
transcripts,annotatedGenome,missing,character-method Man page
transcripts,annotatedGenome,missing,missing-method Man page
txLength Man page
txLength,character,missing,annotatedGenome-method Man page
txLength-methods Man page
txLength,missing,character,annotatedGenome-method Man page
txLength,missing,data.frame,annotatedGenome-method Man page
txLength,missing,missing,annotatedGenome-method Man page
variants Man page
variants<- Man page
variants<-,denovoGeneExpr-method Man page
variants,denovoGeneExpr-method Man page
variants,denovoGenomeExpr-method Man page
wrapDenovo Man page
wrapKnown Man page

Files

DESCRIPTION
NAMESPACE
R
R/ClassDefinitions.R R/GenericDefs.R R/asymmetryCheck.R R/calcDenovo.R R/calcExp.R R/casperVignettes.R R/checks.R R/createDenovoGenome.R R/denovoExpr.R R/genePlot.R R/getDistrs.R R/getRoc.R R/makeTranscriptDbFromGFF.R R/mergeBatches.R R/mergeExp.R R/modelPrior.R R/pathCounts.R R/probNonEquiv.R R/procBam.R R/procGenome.R R/qqnormGenomeWide.R R/relexprByGene.R R/rmShortInserts.R R/simMultSamples.R R/simPost.R R/simReads.R R/splitGenomeByLength.R R/truncnorm.R R/wrapDenovo.R R/wrapKnown.R
build
build/vignette.rds
data
data/K562.r1l1.RData
data/datalist
data/distrsGSE37704.RData
data/hg19DB.RData
inst
inst/CITATION
inst/doc
inst/doc/DesignRNASeq.pdf
inst/doc/casper.R
inst/doc/casper.Rnw
inst/doc/casper.pdf
man
man/K562.r1l1.Rd man/annotatedGenome-class.Rd man/asymmetryCheck.Rd man/calcDenovo.Rd man/calcExp.Rd man/denovoExpr.Rd man/denovoGeneExpr-class.Rd man/denovoGenomeExpr-class.Rd man/distrsGSE37704.Rd man/genePlot.Rd man/getDistrs.Rd man/getIsland.Rd man/getNreads.Rd man/getReads.Rd man/getRoc.Rd man/hg19DB.Rd man/mergeBatches.Rd man/mergeExp.Rd man/modelPrior.Rd man/modelPriorAS-class.Rd man/pathCounts-class.Rd man/pathCounts.Rd man/plot-methods.Rd man/plotExpr.Rd man/plotPriorAS.Rd man/probNonEquiv.Rd man/procBam-class.Rd man/procBam.Rd man/procGenome.Rd man/qqnormGenomeWide.Rd man/quantileNorm.Rd man/relexprByGene.Rd man/rmShortInserts.Rd man/simMAE.Rd man/simMAEcheck.Rd man/simMultSamples.Rd man/simReads.Rd man/simulatedSamples-class.Rd man/splitGenomeByLength.Rd man/subsetGenome.Rd man/transcripts.Rd man/txLength-methods.Rd man/wrapDenovo.Rd man/wrapKnown.Rd
src
src/casper.cpp
src/casper.h
src/cppmemory.h
src/cstat.cpp
src/cstat.h
src/dataframe.cpp
src/dataframe.h
src/discretedf.cpp
src/discretedf.h
src/dropVariant.cpp
src/dropVariant.h
src/exon.cpp
src/exon.h
src/fragFunc.c
src/fragFunc.h
src/fragment.cpp
src/fragment.h
src/functions.c
src/functions.h
src/hash.c
src/hash.h
src/header.h
src/join_exons.c
src/makeIslands.c
src/model.cpp
src/model.h
src/model_cmp.cpp
src/model_cmp.h
src/pathCounts.c
src/procBam.c
src/rcasper.cpp
src/rcasper.h
src/seppel.cpp
src/seppel.h
src/simReads.c
src/simReadsfunc.c
src/simReadsfunc.h
src/smartmodeldist.cpp
src/stdafx.h
src/targetver.h
src/uniqQname.c
src/variant.cpp
src/variant.h
src/variant_cmp.cpp
src/variant_cmp.h
vignettes
vignettes/auto
vignettes/auto/casper.el
vignettes/casper.Rnw
vignettes/references.bib

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