Quick start | Introduction | Aligning reads and importing data | Pre-processing the data for analysis | Estimating expression for a set of known variants | Plots and querying an annotatedGenome
Package: casper 2.47.0
David Rossell
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.
Authors:
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
casper/json (API)
| # Install 'casper' in R: |
| install.packages('casper', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- distrsGSE37704 - Estimated read start and insert size distributions from MiSeq data in GEO dataset GSE37704.
- hg19DB - Subset of human genome
- K562.r1l1 - Toy RNA-seq data from RGASP project.
On BioConductor:casper-2.47.0(bioc 3.24)casper-2.46.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologygeneexpressiondifferentialexpressiontranscriptionrnaseqsequencingcpp
Last updated from:2471cc4deb. Checks:5 ERROR, 6 OK, 3 WARNING. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 250 | ||
| linux-devel-arm64 | OK | 372 | ||
| linux-devel-x86_64 | OK | 476 | ||
| source / vignettes | OK | 359 | ||
| linux-release-arm64 | OK | 417 | ||
| linux-release-x86_64 | OK | 558 | ||
| macos-release-arm64 | ERROR | 281 | ||
| macos-release-x86_64 | ERROR | 539 | ||
| macos-oldrel-arm64 | ERROR | 198 | ||
| macos-oldrel-x86_64 | ERROR | 485 | ||
| windows-devel | WARNING | 387 | ||
| windows-release | WARNING | 454 | ||
| windows-oldrel | WARNING | 365 | ||
| wasm-release | OK | 204 |
Exports:as.listasymmetryCheckcalcDenovocalcExpcasperDesigncreateDenovoGenomedenovoExprgenePlotgetChrgetDistrsgetIslandgetNreadsgetReadsgetRoclinesmatchTranscriptsmergeBatchesmergeExpmodelPriorpathCountsplotPriorASposprobprobNonEquivprocBamprocGenomepvalTreatqqgammaGenomeWideqqnormGenomeWidequantileNormrelexprByGenermShortInsertssimMAEsimMAEchecksimMultSamplessimReadssubsetGenometranscriptstxLengthvariantsvariants<-wrapDenovowrapKnown
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemchroncigarillocliclustercodacodetoolscpp11crayoncurlDBIdbplyrDelayedArraydplyrEBarraysfastmapfilelockformatRfutile.loggerfutile.optionsgagagenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluegsubfngtoolshmshttrhttr2IRangesjsonliteKEGGRESTlambda.rlatticelifecyclelimmamagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpillarpkgconfigpngprettyunitsprogressprotopurrrR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraysqldfstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrsVGAMwithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class "annotatedGenome" | annotatedGenome annotatedGenome-class show,annotatedGenome-method |
| Plot asymmetry coefficients for the observed data and compare to those expected under Normality. | asymmetryCheck asymmetryCheck,data.frame-method asymmetryCheck,ExpressionSet-method asymmetryCheck,matrix-method |
| Estimate expression of gene splicing variants de novo. | calcDenovo |
| Estimate expression of a known set of gene splicing variants. | calcExp |
| Estimate expression for de novo splicing variants. | denovoExpr |
| Class "denovoGeneExpr" | denovoGeneExpr-class names,denovoGenomeExpr-method posprob posprob,denovoGeneExpr-method show,denovoGeneExpr-method variants variants,denovoGeneExpr-method variants,denovoGenomeExpr-method variants<- variants<-,denovoGeneExpr-method [,denovoGeneExpr,ANY,ANY,ANY-method [[,denovoGeneExpr,ANY,ANY,ANY-method [[,denovoGeneExpr,ANY,ANY-method [[,denovoGenomeExpr,ANY,ANY-method |
| Class "denovoGenomeExpr" | as.list,denovoGenomeExpr-method denovoGenomeExpr-class show,denovoGenomeExpr-method [,denovoGenomeExpr,ANY,ANY,ANY-method [[,denovoGenomeExpr-method |
| Estimated read start and insert size distributions from MiSeq data in GEO dataset GSE37704. | distrsGSE37704 |
| Plot exon structure for each transcript of a given gene. | genePlot genePlot,CompressedIRangesList,ANY,ANY,ANY,ANY-method genePlot,GRanges,ANY,ANY,ANY,ANY-method genePlot,GRangesList,ANY,ANY,ANY,ANY-method genePlot,IRanges,ANY,ANY,ANY,ANY-method genePlot,IRangesList,ANY,ANY,ANY,ANY-method genePlot,missing,character,annotatedGenome,GRanges,ExpressionSet-method genePlot,missing,character,annotatedGenome,missing,missing-method genePlot,missing,character,annotatedGenome,procBam,ExpressionSet-method genePlot,missing,character,annotatedGenome,procBam,missing-method genePlot-methods |
| Compute fragment start and fragment length distributions | getDistrs |
| getIsland returns the island id associated to a given entrez or transcript id in an annotatedGenome object. getChr indicates the chromosome for a given Entrez, transcript or island id. | getChr getChr,character,missing,missing,annotatedGenome-method getChr,missing,character,missing,annotatedGenome-method getChr,missing,missing,character,annotatedGenome-method getChr,missing,missing,missing,annotatedGenome-method getChr-method getIsland getIsland,character,missing,annotatedGenome-method getIsland,missing,character,annotatedGenome-method |
| Get total number of paths in each island from a pathCounts object. | getNreads getNreads,pathCounts-method |
| getReads returns the reads stored in a 'procBam' object. | getReads getReads,procBam-method |
| Operating characteristics of differential expression analysis | getRoc getRoc,logical,logical-method getRoc,matrix,matrix-method getRoc,numeric,numeric-method |
| Subset of human genome (UCSC hg19 version) | hg19DB |
| Toy RNA-seq data from RGASP project. | K562.r1l1 |
| Merge two ExpressionSet objects by doing quantile normalization and computing partial residuals (i.e. substracting group mean expression in each batch). As currently implemented the method is only valid for balanced designs, e.g. each batch has the same number of samples per group. | mergeBatches mergeBatches,ExpressionSet,ExpressionSet-method mergeBatches,ExpressionSet,simulatedSamples-method |
| Merge splicing variant expression from multiple samples | mergeExp |
| Set prior distribution on expressed splicing variants. | modelPrior |
| Class "modelPriorAS" | coef,modelPriorAS,ANY,ANY,ANY-method coef,modelPriorAS-method modelPriorAS-class show,modelPriorAS-method [,modelPriorAS,ANY,ANY,ANY-method |
| Compute exon path counts | pathCounts pathCounts,list-method pathCounts,procBam-method pathCounts-method |
| Class "pathCounts" | pathCounts-class show,pathCounts-method |
| Plot estimated read start and fragment length distributions. | lines lines,readDistrs-method plot plot,readDistrs,ANY-method plot,readDistrsList,ANY-method |
| Plot inferred gene structure and expression. | plotExpr plotExpr,denovoGeneExpr-method plotExpr-methods |
| Plot prior distribution on set of expressed variants (i.e. the model space). | plotPriorAS plotPriorAS,modelPriorAS-method plotPriorAS-methods |
| 'probNonEquiv' performs a Bayesian hypothesis test for equivalence between group means. It returns the posterior probability that |mu1-mu2|>logfc. 'pvalTreat' is a wrapper to 'treat' in package 'limma', which returns P-values for the same hypothesis test. | probNonEquiv probNonEquiv,ExpressionSet-method probNonEquiv,list-method pvalTreat pvalTreat,ExpressionSet-method pvalTreat,list-method |
| Process BAM object | procBam procBam,ANY-method procBam,list,logical,integer,logical,character-method procBam,list,logical,integer,logical,missing-method procBam,list,logical,integer,missing,missing-method procBam,list,logical,missing,logical,missing-method procBam,list,logical,missing,missing,missing-method procBam,list,missing,integer,logical,missing-method procBam,list,missing,integer,missing,missing-method procBam,list,missing,missing,logical,missing-method procBam,list,missing,missing,missing,missing-method procBam,list,missing,numeric,missing,missing-method procBam-method |
| Class "procBam" | procBam-class show,procBam-method |
| Create an annotatedGenome object that stores information about genes and transcripts | createDenovoGenome procGenome procGenome,GRanges,ANY-method procGenome,GRanges-method procGenome,TxDb,ANY-method procGenome,TxDb-method |
| Genome-wide qq-normal and qq-gamma plots | qqgammaGenomeWide qqgammaGenomeWide,data.frame-method qqgammaGenomeWide,ExpressionSet-method qqgammaGenomeWide,matrix-method qqnormGenomeWide qqnormGenomeWide,data.frame-method qqnormGenomeWide,ExpressionSet-method qqnormGenomeWide,matrix-method |
| Apply quantile normalization | quantileNorm quantileNorm,ExpressionSet-method quantileNorm,matrix-method |
| Compute relative expressions within each gene | relexprByGene |
| Remove reads with short insert sizes from imported BAM files. | rmShortInserts |
| Simulate Mean Absolute Error (MAE) in estimating isoform expression under various experimental settings. | simMAE |
| Model checking for One Sample Problems. | simMAEcheck |
| Simulate paired end reads for multiple future samples based on pilot data, and obtain their expression estimates via casper | casperDesign simMultSamples |
| Function to simulate paired end reads following given read start and fragment length distributions and gene and variant expressions. | simReads |
| Class "simulatedSamples" | coef,simulatedSamples-method exprs,simulatedSamples-method show,simulatedSamples-method simulatedSamples-class [,simulatedSamples,ANY,ANY,ANY-method [,simulatedSamples,missing,index,missing-method |
| Split an annotatedGenome object into subsets according to gene length | splitGenomeByLength |
| subsetGenome subsets an object of class annotatedGenome for a set of island IDs or chromosome names. | subsetGenome subsetGenome,character,missing,annotatedGenome-method subsetGenome,missing,character,annotatedGenome-method subsetGenome-methods |
| Extracts transcript information (exon start and ends) from an 'annotatedGenome' object, either for all transcripts or only those corresponding to a given island or transcript. | matchTranscripts transcripts transcripts,annotatedGenome,character,missing-method transcripts,annotatedGenome,missing,character-method transcripts,annotatedGenome,missing,missing-method |
| ~~ Methods for Function 'txLength' in Package 'casper' ~~ | txLength txLength,character,missing,annotatedGenome-method txLength,missing,character,annotatedGenome-method txLength,missing,data.frame,annotatedGenome-method txLength,missing,missing,annotatedGenome-method txLength-methods |
| Run all necessary steps to get expression estimates from multiple bam files with the casper pipeline. | wrapDenovo |
| Run all necessary steps to get expression estimates from multiple bam files with the casper pipeline. | wrapKnown |
