SGSeq: Splice event prediction and quantification from RNA-seq data
Version 1.10.0

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.

AuthorLeonard Goldstein
Bioconductor views AlternativeSplicing RNASeq Transcription
Date of publicationNone
MaintainerLeonard Goldstein <goldstel@gene.com>
LicenseArtistic-2.0
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SGSeq")

Getting started

Splice event prediction and quantification from RNA-seq data

Popular man pages

plotCoverage: Plot read coverage and splice junction read counts
plotSpliceGraph: Plot splice graph
plotVariants: Plot splice graph and heatmap of splice variant frequencies
predictVariantEffects: Predict the effect of splice variants on protein-coding...
sgf_pred: Example splice graph features (predicted)
slots: Accessing and replacing metadata columns
tx: Example transcripts
See all...

All man pages Function index File listing

Man pages

analyzeFeatures: Analysis of splice graph features from BAM files
analyzeVariants: Analysis of splice variants
annotate: Annotation with respect to transcript features
annotateSGVariants: Annotate splice variants in terms of canonical events
assays: Accessing and replacing assay data
convertToSGFeatures: Convert transcript features to splice graph features
convertToTxFeatures: Convert to TxFeatures object
exonCompatible: Compatible fragment counts for exons
exportFeatures: Export to BED format
filterFeatures: Filter predicted features
findOverlapsRanges: Modified 'findOverlaps' function for 'IRanges', 'IRangesList'...
findSGVariants: Identify splice variants from splice graph
getBamInfo: Obtain library information from BAM files
getSGFeatureCounts: Compatible counts for splice graph features from BAM files
getSGFeatureCountsPerSample: Compatible fragment counts for splice graph features
getSGVariantCounts: Representative counts and frequency estimates for splice...
gr: Example genomic region of interest
importTranscripts: Import transcripts from GFF file
junctionCompatible: Compatible fragment counts for splice junctions
makeSGFeatureCounts: Create 'SGFeatureCounts' object
makeVariantNames: Create interpretable splice variant names
mergeTxFeatures: Merge redundant features
plotCoverage: Plot read coverage and splice junction read counts
plotFeatures: Plot splice graph and heatmap of expression values
plotSpliceGraph: Plot splice graph
plotVariants: Plot splice graph and heatmap of splice variant frequencies
predictCandidatesInternal: Identify candidate internal exons
predictCandidatesTerminal: Identify candidate terminal exons
predictExonsInternal: Identify internal exons
predictExonsTerminal: Identify terminal exons
predictJunctions: Identify splice junctions
predictSpliced: Ranges-based identification of splice junctions and exons
predictTxFeatures: Splice junction and exon prediction from BAM files
predictTxFeaturesPerSample: Identification of splice junctions and exons from BAM file
predictTxFeaturesPerStrand: Identification of splice junctions and exons for a given...
predictVariantEffects: Predict the effect of splice variants on protein-coding...
processTerminalExons: Process predicted terminal exons
removeExonsIsolated: Remove exons with no flanking splice junctions
sgf_ann: Example splice graph features (annotation-based)
sgfc_ann: Example splice graph feature counts (annotation-based)
sgfc_pred: Example splice graph feature counts (predicted)
SGFeatureCounts: Splice graph feature counts
SGFeatures: Splice graph features
sgf_pred: Example splice graph features (predicted)
SGSegments: Splice graph segments
sgv_ann: Example splice variants (annotation-based)
SGVariantCounts: Splice graph variant counts
SGVariants: Splice graph variants
sgvc_ann: Example splice variant counts (annotated)
sgvc_ann_from_bam: Example splice variant counts (annotated) from BAM files
sgvc_pred: Example splice variant counts (predicted)
sgvc_pred_from_bam: Example splice variant counts (predicted) from BAM files
sgv_pred: Example splice variants (predicted)
si: Example sample information
slots: Accessing and replacing metadata columns
splicesiteOverlap: Compatible fragment counts for splice sites
tx: Example transcripts
txf_ann: Example transcript features (annotation-based)
TxFeatures: Transcript features
txf_pred: Example transcript features (predicted)
updateObject: Update object

Functions

FPKM Man page
FPKM,SGFeatureCounts-method Man page
FPKM,SGVariantCounts-method Man page
FPKM<- Man page
FPKM<-,SGFeatureCounts-method Man page
SGFeatureCounts Man page Source code
SGFeatures Man page Source code
SGSegments Man page Source code
SGVariantCounts Man page Source code
SGVariants Man page Source code
TxFeatures Man page Source code
XS2strand Source code
addAlpha Source code
addDummyNodes Source code
addDummySpliceSites Source code
addFeatureID Source code
addGeneID Source code
addSourceAndSinkNodes Source code
addSpliceSites Source code
analyzeFeatures Man page Source code
analyzeVariants Man page Source code
annotate Man page Source code
annotateFeatures Source code
annotatePaths Source code
annotateSGVariants Man page Source code
annotateSegments Source code
asGRanges Source code
asGRangesList Source code
assays Man page
calculateSizeFactor Source code
cds Source code
cdsEnd Source code
cdsLeft Source code
cdsRight Source code
cdsStart Source code
checkApplyResultsForErrors Source code
checkBamInfo Source code
checkIdenticalSummarizedExperiment Source code
checkSampleInfo Source code
checkTranscriptFormat Source code
closed3p Man page
closed3p,SGVariantCounts-method Man page
closed3p,SGVariants-method Man page
closed3p<- Man page
closed3p<-,SGVariantCounts-method Man page
closed3p<-,SGVariants-method Man page
closed3pEvent Man page
closed3pEvent,SGVariantCounts-method Man page
closed3pEvent,SGVariants-method Man page
closed3pEvent<- Man page
closed3pEvent<-,SGVariantCounts-method Man page
closed3pEvent<-,SGVariants-method Man page
closed5p Man page
closed5p,SGVariantCounts-method Man page
closed5p,SGVariants-method Man page
closed5p<- Man page
closed5p<-,SGVariantCounts-method Man page
closed5p<-,SGVariants-method Man page
closed5pEvent Man page
closed5pEvent,SGVariantCounts-method Man page
closed5pEvent,SGVariants-method Man page
closed5pEvent<- Man page
closed5pEvent<-,SGVariantCounts-method Man page
closed5pEvent<-,SGVariants-method Man page
co2gr Source code
co2str Source code
collapseFeatures Source code
collapseRows Source code
completeMcols Source code
constructGRangesFromRanges Source code
convertFpkmToCount Source code
convertSlots Source code
convertToSGFeatures Man page Source code
convertToSGSegments Source code
convertToTranscripts Source code
convertToTxFeatures Man page Source code
counts,SGFeatureCounts-method Man page
counts,SGVariantCounts-method Man page
counts<-,SGFeatureCounts-method Man page
counts<-,SGVariantCounts-method Man page
createSGFeaturesFromSGVariants Source code
dropMcols Source code
edges Source code
eventID Man page
eventID,SGVariantCounts-method Man page
eventID,SGVariants-method Man page
eventID<- Man page
eventID<-,SGVariantCounts-method Man page
eventID<-,SGVariants-method Man page
exonCompatible Man page Source code
exonCoverage Source code
exonFrame Source code
exonGraph Source code
exonGraphEdges Source code
exonGraphNodes Source code
exonsOnSameChromAndStrand Source code
expandSGVariantCounts Source code
expandString Source code
expandType Source code
expandUnstrandedRanges Source code
exportFeatures Man page Source code
extractExons Source code
extractFeaturesFromVariants Source code
extractIDs Source code
extractJunctions Source code
extractRangesFromFeatures Source code
extractSplicesitesFromJunctions Source code
feature2name Source code
featureID Man page
featureID,Counts-method Man page
featureID,Paths-method Man page
featureID,SGFeatures-method Man page
featureID3p Man page
featureID3p,SGVariantCounts-method Man page
featureID3p,SGVariants-method Man page
featureID3p<- Man page
featureID3p<-,SGVariantCounts-method Man page
featureID3p<-,SGVariants-method Man page
featureID3pEvent Man page
featureID3pEvent,SGVariantCounts-method Man page
featureID3pEvent,SGVariants-method Man page
featureID3pEvent<- Man page
featureID3pEvent<-,SGVariantCounts-method Man page
featureID3pEvent<-,SGVariants-method Man page
featureID5p Man page
featureID5p,SGVariantCounts-method Man page
featureID5p,SGVariants-method Man page
featureID5p<- Man page
featureID5p<-,SGVariantCounts-method Man page
featureID5p<-,SGVariants-method Man page
featureID5pEvent Man page
featureID5pEvent,SGVariantCounts-method Man page
featureID5pEvent,SGVariants-method Man page
featureID5pEvent<- Man page
featureID5pEvent<-,SGVariantCounts-method Man page
featureID5pEvent<-,SGVariants-method Man page
featureID<- Man page
featureID<-,Counts-method Man page
featureID<-,Paths-method Man page
featureID<-,SGFeatures-method Man page
filterExonsInternal Source code
filterExonsTerminal Source code
filterFeatures Man page Source code
filterGa Source code
filterGap Source code
filterIntrons Source code
filterJunctions Source code
findAllPaths Source code
findCDS Source code
findEvents Source code
findOverlapsRanges Man page Source code
findSGSegments Source code
findSGSegmentsPerGene Source code
findSGVariants Man page Source code
findSGVariantsFromSGFeatures Source code
findVariantsPerGene Source code
from,Paths-method Man page
from,SGVariantCounts-method Man page
from<- Man page
from<-,Paths-method Man page
from<-,SGVariantCounts-method Man page
geneID Man page
geneID,Counts-method Man page
geneID,Paths-method Man page
geneID,SGFeatures-method Man page
geneID<- Man page
geneID<-,Counts-method Man page
geneID<-,Paths-method Man page
geneID<-,SGFeatures-method Man page
geneName Man page
geneName,Counts-method Man page
geneName,Features-method Man page
geneName,Paths-method Man page
geneName<- Man page
geneName<-,Counts-method Man page
geneName<-,Features-method Man page
geneName<-,Paths-method Man page
generateCompleteMessage Source code
generateWarningMessage Source code
getBamInfo Man page Source code
getBamInfoPerSample Source code
getCoverage Source code
getCoveragePerSample Source code
getEffectiveLengths Source code
getEventLocation Source code
getExonCoordinates Source code
getFeatureLengths Source code
getGraphInfo Source code
getHGVSDeletion Source code
getHGVSFlanking Source code
getHGVSInsertion Source code
getHGVSRefPos Source code
getHGVSRefPosIntronic Source code
getHGVSVariantDeletionInsertion Source code
getHGVSVariantFrameshift Source code
getHGVSVariantNTerminalExtension Source code
getHGVSVariantNTerminalVariant Source code
getHGVSVariantNoProtein Source code
getHGVSVariantProteinUnaffected Source code
getHGVSVariantRNA Source code
getLayoutParameters Source code
getPadding Source code
getProteinSeq Source code
getRNASeq Source code
getRepresentativeFeatureIDs Source code
getSGFeatureCounts Man page Source code
getSGFeatureCountsPerSample Man page Source code
getSGFeatureCountsPerStrand Source code
getSGVariantCounts Man page Source code
getSGVariantCountsFromBamFiles Source code
getSGVariantCountsFromSGFeatureCounts Source code
getSGVariantCountsPerSample Source code
getSGVariantCountsPerStrand Source code
getScaledCounts Source code
getTerminalFeatureIDs Source code
getVariant Source code
getVariantFreq Source code
getVariantProtein Source code
getVariantRNA Source code
gr Man page
gr2co Source code
gr2pos Source code
importTranscripts Man page Source code
isOr Source code
junctionCompatible Man page Source code
makeCompleteMessage Source code
makeErrorMessage Source code
makeSGFeatureCounts Man page Source code
makeSGVariantCounts Source code
makeVariantNames Man page Source code
makeWarningMessage Source code
mapEventToProtein Source code
mapVariantsToTranscripts Source code
maskInnerEvents Source code
matchExon Source code
matchJunction Source code
matchSGFeatures Source code
matchSplice Source code
matchTxFeatures Source code
mergeExonsTerminal Source code
mergeSGFeatures Source code
mergeTxFeatures Man page Source code
neighborhood2 Source code
nextFrame Source code
nodes Source code
pfirst Source code
pintersect Source code
plast Source code
plotCoverage Man page Source code
plotExonGraph Source code
plotFeatures Man page Source code
plotImage Source code
plotRanges Source code
plotSpliceGraph Man page Source code
plotTrackRanges Source code
plotTrackScore Source code
plotVariants Man page Source code
pos2gr Source code
pos2str Source code
predictCandidatesInternal Man page Source code
predictCandidatesTerminal Man page Source code
predictExonsInternal Man page Source code
predictExonsTerminal Man page Source code
predictJunctions Man page Source code
predictSpliced Man page Source code
predictTxFeatures Man page Source code
predictTxFeaturesPerSample Man page Source code
predictTxFeaturesPerStrand Man page Source code
predictVariantEffectPerVariantAndTranscript Source code
predictVariantEffects Man page Source code
processFeatures Source code
processTerminalExons Man page Source code
processTranscripts Source code
propagateAnnotation Source code
propagateXS Source code
punion Source code
rbindDfsWithoutRowNames Source code
rbindListOfDFs Source code
readGap Source code
reindex Source code
removeExonsIsolated Man page Source code
reorderFeatures Source code
restrictFeatures Source code
scorePerExon Source code
segmentID Man page
segmentID,Paths-method Man page
segmentID,SGVariantCounts-method Man page
segmentID<- Man page
segmentID<-,Paths-method Man page
segmentID<-,SGVariantCounts-method Man page
selectFeatures Source code
setCores Source code
setFeatureColors Source code
setPreschedule Source code
sgf_ann Man page
sgf_pred Man page
sgfc_ann Man page
sgfc_pred Man page
sgv_ann Man page
sgv_pred Man page
sgvc_ann Man page
sgvc_ann_from_bam Man page
sgvc_pred Man page
sgvc_pred_from_bam Man page
si Man page
silent_select Source code
slots Man page
sortEvents Source code
splice3p Man page
splice3p,SGFeatureCounts-method Man page
splice3p,SGFeatures-method Man page
splice3p,SGSegments-method Man page
splice3p<- Man page
splice3p<-,SGFeatureCounts-method Man page
splice3p<-,SGFeatures-method Man page
splice3p<-,SGSegments-method Man page
splice5p Man page
splice5p,SGFeatureCounts-method Man page
splice5p,SGFeatures-method Man page
splice5p,SGSegments-method Man page
splice5p<- Man page
splice5p<-,SGFeatureCounts-method Man page
splice5p<-,SGFeatures-method Man page
splice5p<-,SGSegments-method Man page
spliceGraph Source code
splicesiteCounts Source code
splicesiteOverlap Man page Source code
splitCharacterList Source code
subgraph Source code
to,Paths-method Man page
to,SGVariantCounts-method Man page
to<- Man page
to<-,Paths-method Man page
to<-,SGVariantCounts-method Man page
tx Man page
txName Man page
txName,Counts-method Man page
txName,Features-method Man page
txName,Paths-method Man page
txName<- Man page
txName<-,Counts-method Man page
txName<-,Features-method Man page
txName<-,Paths-method Man page
txf_ann Man page
txf_pred Man page
type,Counts-method Man page
type,Features-method Man page
type,Paths-method Man page
type<- Man page
type<-,Counts-method Man page
type<-,Features-method Man page
type<-,Paths-method Man page
typeLevels Source code
uniqueFeatures Source code
unmaskEvents Source code
updateObject Man page
updateObject,SGVariantCounts-method Man page
updateObject,SGVariants-method Man page
validAssays Source code
validExtraColumnSlotLengths Source code
validExtraColumnSlotValues Source code
validMcols Source code
validSGFeatureCounts Source code
validSGFeatures Source code
validSGSegments Source code
validSGVariantCounts Source code
validSGVariants Source code
validTxFeatures Source code
validValues Source code
variantFreq Man page
variantFreq,SGVariantCounts-method Man page
variantFreq<- Man page
variantFreq<-,SGVariantCounts-method Man page
variantID Man page
variantID,SGVariantCounts-method Man page
variantID,SGVariants-method Man page
variantID<- Man page
variantID<-,SGVariantCounts-method Man page
variantID<-,SGVariants-method Man page
variantName Man page
variantName,SGVariantCounts-method Man page
variantName,SGVariants-method Man page
variantName<- Man page
variantName<-,SGVariantCounts-method Man page
variantName<-,SGVariants-method Man page
variantType Man page
variantType,SGVariantCounts-method Man page
variantType,SGVariants-method Man page
variantType<- Man page
variantType<-,SGVariantCounts-method Man page
variantType<-,SGVariants-method Man page
xcoordinates Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/annotation.R
R/classes.R
R/convert.R
R/counts.R
R/data.R
R/features-filter.R
R/features-merge.R
R/features-prediction.R
R/graphs.R
R/main.R
R/misc.R
R/overlaps.R
R/plots.R
R/sequences.R
R/slots-generics.R
R/slots-methods.R
build
build/vignette.rds
data
data/gr.rda
data/sgf_ann.rda
data/sgf_pred.rda
data/sgfc_ann.rda
data/sgfc_pred.rda
data/sgv_ann.rda
data/sgv_pred.rda
data/sgvc_ann.rda
data/sgvc_ann_from_bam.rda
data/sgvc_pred.rda
data/sgvc_pred_from_bam.rda
data/si.rda
data/tx.rda
data/txf_ann.rda
data/txf_pred.rda
inst
inst/CITATION
inst/doc
inst/doc/SGSeq.R
inst/doc/SGSeq.Rmd
inst/doc/SGSeq.html
inst/extdata
inst/extdata/bams
inst/extdata/bams/N1.bam
inst/extdata/bams/N1.bam.bai
inst/extdata/bams/N2.bam
inst/extdata/bams/N2.bam.bai
inst/extdata/bams/N3.bam
inst/extdata/bams/N3.bam.bai
inst/extdata/bams/N4.bam
inst/extdata/bams/N4.bam.bai
inst/extdata/bams/T1.bam
inst/extdata/bams/T1.bam.bai
inst/extdata/bams/T2.bam
inst/extdata/bams/T2.bam.bai
inst/extdata/bams/T3.bam
inst/extdata/bams/T3.bam.bai
inst/extdata/bams/T4.bam
inst/extdata/bams/T4.bam.bai
inst/scripts
inst/scripts/createExampleData.R
inst/unitTests
inst/unitTests/test_analyzeFeatures.R
inst/unitTests/test_analyzeVariants.R
inst/unitTests/test_annotate.R
inst/unitTests/test_classes.R
inst/unitTests/test_convertToSGFeatures.R
inst/unitTests/test_convertToTxFeatures.R
inst/unitTests/test_findSGVariants.R
inst/unitTests/test_getBamInfo.R
inst/unitTests/test_getSGFeatureCounts.R
inst/unitTests/test_getSGVariantCounts.R
inst/unitTests/test_mergeTxFeatures.R
inst/unitTests/test_predictTxFeatures.R
inst/unitTests/test_predictVariantEffects.R
man
man/SGFeatureCounts.Rd
man/SGFeatures.Rd
man/SGSegments.Rd
man/SGVariantCounts.Rd
man/SGVariants.Rd
man/TxFeatures.Rd
man/analyzeFeatures.Rd
man/analyzeVariants.Rd
man/annotate.Rd
man/annotateSGVariants.Rd
man/assays.Rd
man/convertToSGFeatures.Rd
man/convertToTxFeatures.Rd
man/exonCompatible.Rd
man/exportFeatures.Rd
man/filterFeatures.Rd
man/findOverlapsRanges.Rd
man/findSGVariants.Rd
man/getBamInfo.Rd
man/getSGFeatureCounts.Rd
man/getSGFeatureCountsPerSample.Rd
man/getSGVariantCounts.Rd
man/gr.Rd
man/importTranscripts.Rd
man/junctionCompatible.Rd
man/makeSGFeatureCounts.Rd
man/makeVariantNames.Rd
man/mergeTxFeatures.Rd
man/plotCoverage.Rd
man/plotFeatures.Rd
man/plotSpliceGraph.Rd
man/plotVariants.Rd
man/predictCandidatesInternal.Rd
man/predictCandidatesTerminal.Rd
man/predictExonsInternal.Rd
man/predictExonsTerminal.Rd
man/predictJunctions.Rd
man/predictSpliced.Rd
man/predictTxFeatures.Rd
man/predictTxFeaturesPerSample.Rd
man/predictTxFeaturesPerStrand.Rd
man/predictVariantEffects.Rd
man/processTerminalExons.Rd
man/removeExonsIsolated.Rd
man/sgf_ann.Rd
man/sgf_pred.Rd
man/sgfc_ann.Rd
man/sgfc_pred.Rd
man/sgv_ann.Rd
man/sgv_pred.Rd
man/sgvc_ann.Rd
man/sgvc_ann_from_bam.Rd
man/sgvc_pred.Rd
man/sgvc_pred_from_bam.Rd
man/si.Rd
man/slots.Rd
man/splicesiteOverlap.Rd
man/tx.Rd
man/txf_ann.Rd
man/txf_pred.Rd
man/updateObject.Rd
tests
tests/runTests.R
vignettes
vignettes/SGSeq.Rmd
vignettes/SGSeq.bib
vignettes/classes.pdf
vignettes/classes.png
SGSeq documentation built on May 20, 2017, 10:32 p.m.

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