Package: EventPointer 3.13.0
Juan A. Ferrer-Bonsoms
EventPointer: An effective identification of alternative splicing events using junction arrays and RNA-Seq data
EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.
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EventPointer.pdf |EventPointer.html✨
EventPointer/json (API)
NEWS
| # Install 'EventPointer' in R: |
| install.packages('EventPointer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jpromeror/eventpointer/issues
- AllEvents_RNASeq - Alternative splicing events detected by EventPointer
- AllEvents_RNASeq_MP - Alternative splicing multi-path events detected by EventPointer
- ArrayDatamultipath - Preprocessed arrays data with multi-path events
- ArraysData - Preprocessed arrays data
- EventXtrans - Relationship between isoforms and events
- Fit - Result of EventPointer_Bootstrap
- MyPrimers - Data frame with primers design for conventional PCR
- MyPrimers_taqman - Data frame with primers design for taqman PCR
- PSIss - Relationship between isoforms and events
- SG_RNASeq - Splicing graph elements predicted from BAM files
- SG_reclassify - Splicing graph example for Events_ReClassification function
- TxD - Transcript x Protein Domain matrix: small matrix for examples
On BioConductor:EventPointer-3.13.0(bioc 3.20)EventPointer-3.12.0(bioc 3.19)
Last updated 2 months agofrom:6c3c36a3ea
Exports:CDFfromGTFCDFfromGTF_MultipathEventDetectionEventDetection_transcriptomeEventDetectionMultipathEventPointerEventPointer_BootstrapsEventPointer_IGVEventPointer_RNASeqEventPointer_RNASeq_IGVEventPointer_RNASeq_TranRefEventPointer_RNASeq_TranRef_IGVEvents_ReClassificationFindPrimersgetbootstrapdataGetPSI_FromTranRefPrepareBam_EPProtein_Domain_EnrichmentPSI_StatisticResulTable
Dependencies:abindaffxparserAnnotationDbiaskpassBHbiglmBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicobscodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIDelayedArraydiagramdigestdoParallelfansifarverfastmapfastmatchfgseaforeachformatRfutile.loggerfutile.optionsfuturefuture.applyGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glmnetglobalsgluegraphgtablehttrigraphIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelavalifecyclelimmalistenvlpSolvemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmimemunsellnlmennlsnumDerivopensslparallellypillarpkgconfigplogrplyrpngpoibinprodlimprogressrquantregqvalueR6RBGLRColorBrewerRcppRcppEigenRCurlreshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLitertracklayerRUnitS4ArraysS4VectorsscalesSGSeqshapesnowSparseArraySparseMspeedglmSQUAREMstatmodstringistringrSummarizedExperimentsurvivalsystibbletximportUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
