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.

AuthorDavid Rossell, Camille Stephan-Otto, Manuel Kroiss, Miranda Stobbe, Victor Pena
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...

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

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