Overview | Preliminaries | RNA transcripts and the TxFeatures class | The splice graph and the SGFeatures class | Splice graph analysis based on annotated transcripts | Splice graph analysis based on de novo prediction | Splice variant identification | Splice variant quantification | Splice variant interpretation | Visualization | Testing for differential splice variant usage | Advanced usage | Multi-core use and memory requirements | Session information | References
Package: SGSeq 1.47.0
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:
SGSeq_1.47.0.tar.gz
SGSeq_1.47.0.zip(r-4.7)SGSeq_1.47.0.zip(r-4.6)SGSeq_1.47.0.zip(r-4.5)
SGSeq_1.47.0.tgz(r-4.6-any)SGSeq_1.47.0.tgz(r-4.5-any)
SGSeq_1.47.0.tar.gz(r-4.7-any)SGSeq_1.47.0.tar.gz(r-4.6-any)
SGSeq_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SGSeq/json (API)
| # Install 'SGSeq' in R: |
| install.packages('SGSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:SGSeq-1.47.0(bioc 3.24)SGSeq-1.46.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
alternativesplicingimmunooncologyrnaseqtranscription
Last updated from:64bc43b811. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
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| bioc-checks | WARNING | 284 | ||
| linux-devel-x86_64 | NOTE | 657 | ||
| source / vignettes | OK | 546 | ||
| linux-release-x86_64 | NOTE | 632 | ||
| macos-release-arm64 | NOTE | 414 | ||
| macos-oldrel-arm64 | NOTE | 368 | ||
| windows-devel | NOTE | 612 | ||
| windows-release | NOTE | 563 | ||
| windows-oldrel | NOTE | 597 | ||
| wasm-release | OK | 258 |
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:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrigraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerRUnitS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysUCSC.utilsvctrsXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Analysis of splice graph features from BAM files | analyzeFeatures |
| Analysis of splice variants | analyzeVariants |
| Annotation with respect to transcript features | annotate |
| Accessing and replacing assay data | assays 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 features | convertToSGFeatures |
| Convert to TxFeatures object | convertToTxFeatures |
| Export to BED format | exportFeatures |
| Identify splice variants from splice graph | findSGVariants |
| Obtain library information from BAM files | getBamInfo |
| Compatible counts for splice graph features from BAM files | getSGFeatureCounts |
| Representative counts and frequency estimates for splice variants | getSGVariantCounts |
| Import transcripts from GFF file | importTranscripts |
| Create 'SGFeatureCounts' object | makeSGFeatureCounts |
| Merge redundant features | mergeTxFeatures |
| Plot read coverage and splice junction read counts | plotCoverage |
| Plot splice graph and heatmap of expression values | plotFeatures |
| Plot splice graph | plotSpliceGraph |
| Plot splice graph and heatmap of splice variant frequencies | plotVariants |
| Splice junction and exon prediction from BAM files | predictTxFeatures |
| Predict the effect of splice variants on protein-coding transcripts | predictVariantEffects |
| Process predicted terminal exons | processTerminalExons |
| Splice graph feature counts | SGFeatureCounts |
| Splice graph features | SGFeatures |
| Splice graph variant counts | SGVariantCounts |
| Splice graph variants | SGVariants |
| Accessing and replacing metadata columns | closed3p 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 features | TxFeatures |
| Update object | updateObject updateObject,SGVariantCounts-method updateObject,SGVariants-method |
