Package: SGSeq 1.41.0

Leonard Goldstein

SGSeq: Splice event prediction and quantification from RNA-seq data

SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.

Authors:Leonard Goldstein [cre, aut]

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SGSeq.pdf |SGSeq.html✨
SGSeq/json (API)
NEWS

# Install 'SGSeq' in R:
install.packages('SGSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

    On BioConductor:SGSeq-1.41.0(bioc 3.21)SGSeq-1.40.0(bioc 3.20)

    This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

    alternativesplicingimmunooncologyrnaseqtranscription

    5.90 score 3 packages 44 scripts 650 downloads 14 mentions 77 exports 71 dependencies

    Last updated 21 days agofrom:193e8a3f30. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKOct 31 2024
    R-4.5-winWARNINGOct 31 2024
    R-4.5-linuxNOTEOct 31 2024
    R-4.4-winWARNINGOct 31 2024
    R-4.4-macNOTEOct 31 2024
    R-4.3-winWARNINGOct 31 2024
    R-4.3-macNOTEOct 31 2024

    Exports:analyzeFeaturesanalyzeVariantsannotateclosed3pclosed3p<-closed3pEventclosed3pEvent<-closed5pclosed5p<-closed5pEventclosed5pEvent<-convertToSGFeaturesconvertToTxFeaturescountscounts<-eventIDeventID<-exportFeaturesfeatureIDfeatureID<-featureID3pfeatureID3p<-featureID3pEventfeatureID3pEvent<-featureID5pfeatureID5p<-featureID5pEventfeatureID5pEvent<-findSGVariantsFPKMFPKM<-fromfrom<-geneIDgeneID<-geneNamegeneName<-getBamInfogetSGFeatureCountsgetSGVariantCountsimportTranscriptsmakeSGFeatureCountsmakeVariantNamesmergeTxFeaturesplotCoverageplotFeaturesplotSpliceGraphplotVariantspredictTxFeaturespredictVariantEffectsprocessTerminalExonssegmentIDsegmentID<-SGFeatureCountsSGFeaturesSGVariantCountsSGVariantssplice3psplice3p<-splice5psplice5p<-toto<-TxFeaturestxNametxName<-typetype<-updateObjectvariantFreqvariantFreq<-variantIDvariantID<-variantNamevariantName<-variantTypevariantType<-

    Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrigraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerRUnitS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryamlzlibbioc

    Splice event prediction and quantification from RNA-seq data

    Leonard D Goldstein

    Rendered fromSGSeq.Rmdusingknitr::rmarkdownon Oct 31 2024.

    Last update: 2019-05-13
    Started: 2015-10-10

    Readme and manuals

    Help Manual

    Help pageTopics
    Analysis of splice graph features from BAM filesanalyzeFeatures
    Analysis of splice variantsanalyzeVariants
    Annotation with respect to transcript featuresannotate
    Accessing and replacing assay dataassays counts,SGFeatureCounts-method counts,SGVariantCounts-method counts<-,SGFeatureCounts-method counts<-,SGVariantCounts-method FPKM FPKM,SGFeatureCounts-method FPKM,SGVariantCounts-method FPKM<- FPKM<-,SGFeatureCounts-method variantFreq variantFreq,SGVariantCounts-method variantFreq<- variantFreq<-,SGVariantCounts-method
    Convert transcript features to splice graph featuresconvertToSGFeatures
    Convert to TxFeatures objectconvertToTxFeatures
    Export to BED formatexportFeatures
    Identify splice variants from splice graphfindSGVariants
    Obtain library information from BAM filesgetBamInfo
    Compatible counts for splice graph features from BAM filesgetSGFeatureCounts
    Representative counts and frequency estimates for splice variantsgetSGVariantCounts
    Import transcripts from GFF fileimportTranscripts
    Create 'SGFeatureCounts' objectmakeSGFeatureCounts
    Merge redundant featuresmergeTxFeatures
    Plot read coverage and splice junction read countsplotCoverage
    Plot splice graph and heatmap of expression valuesplotFeatures
    Plot splice graphplotSpliceGraph
    Plot splice graph and heatmap of splice variant frequenciesplotVariants
    Splice junction and exon prediction from BAM filespredictTxFeatures
    Predict the effect of splice variants on protein-coding transcriptspredictVariantEffects
    Process predicted terminal exonsprocessTerminalExons
    Splice graph feature countsSGFeatureCounts
    Splice graph featuresSGFeatures
    Splice graph variant countsSGVariantCounts
    Splice graph variantsSGVariants
    Accessing and replacing metadata columnsclosed3p closed3p,SGVariantCounts-method closed3p,SGVariants-method closed3p<- closed3p<-,SGVariantCounts-method closed3p<-,SGVariants-method closed3pEvent closed3pEvent,SGVariantCounts-method closed3pEvent,SGVariants-method closed3pEvent<- closed3pEvent<-,SGVariantCounts-method closed3pEvent<-,SGVariants-method closed5p closed5p,SGVariantCounts-method closed5p,SGVariants-method closed5p<- closed5p<-,SGVariantCounts-method closed5p<-,SGVariants-method closed5pEvent closed5pEvent,SGVariantCounts-method closed5pEvent,SGVariants-method closed5pEvent<- closed5pEvent<-,SGVariantCounts-method closed5pEvent<-,SGVariants-method eventID eventID,SGVariantCounts-method eventID,SGVariants-method eventID<- eventID<-,SGVariantCounts-method eventID<-,SGVariants-method featureID featureID,Counts-method featureID,Paths-method featureID,SGFeatures-method featureID3p featureID3p,SGVariantCounts-method featureID3p,SGVariants-method featureID3p<- featureID3p<-,SGVariantCounts-method featureID3p<-,SGVariants-method featureID3pEvent featureID3pEvent,SGVariantCounts-method featureID3pEvent,SGVariants-method featureID3pEvent<- featureID3pEvent<-,SGVariantCounts-method featureID3pEvent<-,SGVariants-method featureID5p featureID5p,SGVariantCounts-method featureID5p,SGVariants-method featureID5p<- featureID5p<-,SGVariantCounts-method featureID5p<-,SGVariants-method featureID5pEvent featureID5pEvent,SGVariantCounts-method featureID5pEvent,SGVariants-method featureID5pEvent<- featureID5pEvent<-,SGVariantCounts-method featureID5pEvent<-,SGVariants-method featureID<- featureID<-,Counts-method featureID<-,Paths-method featureID<-,SGFeatures-method from,Paths-method from,SGVariantCounts-method from<- from<-,Paths-method from<-,SGVariantCounts-method geneID geneID,Counts-method geneID,Paths-method geneID,SGFeatures-method geneID<- geneID<-,Counts-method geneID<-,Paths-method geneID<-,SGFeatures-method geneName geneName,Counts-method geneName,Features-method geneName,Paths-method geneName<- geneName<-,Counts-method geneName<-,Features-method geneName<-,Paths-method segmentID segmentID,Paths-method segmentID,SGVariantCounts-method segmentID<- segmentID<-,Paths-method segmentID<-,SGVariantCounts-method slots splice3p splice3p,SGFeatureCounts-method splice3p,SGFeatures-method splice3p,SGSegments-method splice3p<- splice3p<-,SGFeatureCounts-method splice3p<-,SGFeatures-method splice3p<-,SGSegments-method splice5p splice5p,SGFeatureCounts-method splice5p,SGFeatures-method splice5p,SGSegments-method splice5p<- splice5p<-,SGFeatureCounts-method splice5p<-,SGFeatures-method splice5p<-,SGSegments-method to,Paths-method to,SGVariantCounts-method to<- to<-,Paths-method to<-,SGVariantCounts-method txName txName,Counts-method txName,Features-method txName,Paths-method txName<- txName<-,Counts-method txName<-,Features-method txName<-,Paths-method type,Counts-method type,Features-method type,Paths-method type<- type<-,Counts-method type<-,Features-method type<-,Paths-method variantID variantID,SGVariantCounts-method variantID,SGVariants-method variantID<- variantID<-,SGVariantCounts-method variantID<-,SGVariants-method variantName variantName,SGVariantCounts-method variantName,SGVariants-method variantName<- variantName<-,SGVariantCounts-method variantName<-,SGVariants-method variantType variantType,SGVariantCounts-method variantType,SGVariants-method variantType<- variantType<-,SGVariantCounts-method variantType<-,SGVariants-method
    Transcript featuresTxFeatures
    Update objectupdateObject updateObject,SGVariantCounts-method updateObject,SGVariants-method