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.

Author
David Rossell, Camille Stephan-Otto, Manuel Kroiss, Miranda Stobbe, Victor Pena
Date of publication
None
Maintainer
David Rossell <rosselldavid@gmail.com>
License
GPL (>=2)
Version
2.8.0

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...

Files in this package

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