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 sequence reads mapped to a reference genome in BAM format. Genes are represented as a genome-wide splice graph, which can be obtained from existing annotation or can be predicted from the data. 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 package includes functions for splice event prediction, quantification, visualization and interpretation.

AuthorLeonard Goldstein
Date of publicationNone
MaintainerLeonard Goldstein <goldstel@gene.com>
LicenseArtistic-2.0
Version1.8.1

View on Bioconductor

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

analyzeFeatures Man page
analyzeVariants Man page
annotate Man page
annotateSGVariants Man page
assays Man page
closed3p Man page
closed3p<- Man page
closed3pEvent Man page
closed3pEvent<- Man page
closed3pEvent<-,SGVariantCounts-method Man page
closed3pEvent,SGVariantCounts-method Man page
closed3pEvent<-,SGVariants-method Man page
closed3pEvent,SGVariants-method Man page
closed3p<-,SGVariantCounts-method Man page
closed3p,SGVariantCounts-method Man page
closed3p<-,SGVariants-method Man page
closed3p,SGVariants-method Man page
closed5p Man page
closed5p<- Man page
closed5pEvent Man page
closed5pEvent<- Man page
closed5pEvent<-,SGVariantCounts-method Man page
closed5pEvent,SGVariantCounts-method Man page
closed5pEvent<-,SGVariants-method Man page
closed5pEvent,SGVariants-method Man page
closed5p<-,SGVariantCounts-method Man page
closed5p,SGVariantCounts-method Man page
closed5p<-,SGVariants-method Man page
closed5p,SGVariants-method Man page
convertToSGFeatures Man page
convertToTxFeatures Man page
counts<-,SGFeatureCounts-method Man page
counts,SGFeatureCounts-method Man page
counts<-,SGVariantCounts-method Man page
counts,SGVariantCounts-method Man page
eventID Man page
eventID<- Man page
eventID<-,SGVariantCounts-method Man page
eventID,SGVariantCounts-method Man page
eventID<-,SGVariants-method Man page
eventID,SGVariants-method Man page
exonCompatible Man page
exportFeatures Man page
featureID Man page
featureID<- Man page
featureID3p Man page
featureID3p<- Man page
featureID3pEvent Man page
featureID3pEvent<- Man page
featureID3pEvent<-,SGVariantCounts-method Man page
featureID3pEvent,SGVariantCounts-method Man page
featureID3pEvent<-,SGVariants-method Man page
featureID3pEvent,SGVariants-method Man page
featureID3p<-,SGVariantCounts-method Man page
featureID3p,SGVariantCounts-method Man page
featureID3p<-,SGVariants-method Man page
featureID3p,SGVariants-method Man page
featureID5p Man page
featureID5p<- Man page
featureID5pEvent Man page
featureID5pEvent<- Man page
featureID5pEvent<-,SGVariantCounts-method Man page
featureID5pEvent,SGVariantCounts-method Man page
featureID5pEvent<-,SGVariants-method Man page
featureID5pEvent,SGVariants-method Man page
featureID5p<-,SGVariantCounts-method Man page
featureID5p,SGVariantCounts-method Man page
featureID5p<-,SGVariants-method Man page
featureID5p,SGVariants-method Man page
featureID<-,Counts-method Man page
featureID,Counts-method Man page
featureID<-,Paths-method Man page
featureID,Paths-method Man page
featureID<-,SGFeatures-method Man page
featureID,SGFeatures-method Man page
filterFeatures Man page
findOverlapsRanges Man page
findSGVariants Man page
FPKM Man page
FPKM<- Man page
FPKM<-,SGFeatureCounts-method Man page
FPKM,SGFeatureCounts-method Man page
FPKM,SGVariantCounts-method Man page
from<- Man page
from<-,Paths-method Man page
from,Paths-method Man page
from<-,SGVariantCounts-method Man page
from,SGVariantCounts-method Man page
geneID Man page
geneID<- Man page
geneID<-,Counts-method Man page
geneID,Counts-method Man page
geneID<-,Paths-method Man page
geneID,Paths-method Man page
geneID<-,SGFeatures-method Man page
geneID,SGFeatures-method Man page
geneName Man page
geneName<- Man page
geneName<-,Counts-method Man page
geneName,Counts-method Man page
geneName<-,Features-method Man page
geneName,Features-method Man page
geneName<-,Paths-method Man page
geneName,Paths-method Man page
getBamInfo Man page
getSGFeatureCounts Man page
getSGFeatureCountsPerSample Man page
getSGVariantCounts Man page
gr Man page
importTranscripts Man page
junctionCompatible Man page
makeSGFeatureCounts Man page
makeVariantNames Man page
mergeTxFeatures Man page
plotCoverage Man page
plotFeatures Man page
plotSpliceGraph Man page
plotVariants Man page
predictCandidatesInternal Man page
predictCandidatesTerminal Man page
predictExonsInternal Man page
predictExonsTerminal Man page
predictJunctions Man page
predictSpliced Man page
predictTxFeatures Man page
predictTxFeaturesPerSample Man page
predictTxFeaturesPerStrand Man page
predictVariantEffects Man page
processTerminalExons Man page
removeExonsIsolated Man page
segmentID Man page
segmentID<- Man page
segmentID<-,Paths-method Man page
segmentID,Paths-method Man page
segmentID<-,SGVariantCounts-method Man page
segmentID,SGVariantCounts-method Man page
sgf_ann Man page
sgfc_ann Man page
sgfc_pred Man page
SGFeatureCounts Man page
SGFeatures Man page
sgf_pred Man page
SGSegments Man page
sgv_ann Man page
SGVariantCounts Man page
SGVariants Man page
sgvc_ann Man page
sgvc_ann_from_bam Man page
sgvc_pred Man page
sgvc_pred_from_bam Man page
sgv_pred Man page
si Man page
slots Man page
splice3p Man page
splice3p<- Man page
splice3p<-,SGFeatureCounts-method Man page
splice3p,SGFeatureCounts-method Man page
splice3p<-,SGFeatures-method Man page
splice3p,SGFeatures-method Man page
splice3p<-,SGSegments-method Man page
splice3p,SGSegments-method Man page
splice5p Man page
splice5p<- Man page
splice5p<-,SGFeatureCounts-method Man page
splice5p,SGFeatureCounts-method Man page
splice5p<-,SGFeatures-method Man page
splice5p,SGFeatures-method Man page
splice5p<-,SGSegments-method Man page
splice5p,SGSegments-method Man page
splicesiteOverlap Man page
to<- Man page
to<-,Paths-method Man page
to,Paths-method Man page
to<-,SGVariantCounts-method Man page
to,SGVariantCounts-method Man page
tx Man page
txf_ann Man page
TxFeatures Man page
txf_pred Man page
txName Man page
txName<- Man page
txName<-,Counts-method Man page
txName,Counts-method Man page
txName<-,Features-method Man page
txName,Features-method Man page
txName<-,Paths-method Man page
txName,Paths-method Man page
type<- Man page
type<-,Counts-method Man page
type,Counts-method Man page
type<-,Features-method Man page
type,Features-method Man page
type<-,Paths-method Man page
type,Paths-method Man page
updateObject Man page
updateObject,SGVariantCounts-method Man page
updateObject,SGVariants-method Man page
variantFreq Man page
variantFreq<- Man page
variantFreq<-,SGVariantCounts-method Man page
variantFreq,SGVariantCounts-method Man page
variantID Man page
variantID<- Man page
variantID<-,SGVariantCounts-method Man page
variantID,SGVariantCounts-method Man page
variantID<-,SGVariants-method Man page
variantID,SGVariants-method Man page
variantName Man page
variantName<- Man page
variantName<-,SGVariantCounts-method Man page
variantName,SGVariantCounts-method Man page
variantName<-,SGVariants-method Man page
variantName,SGVariants-method Man page
variantType Man page
variantType<- Man page
variantType<-,SGVariantCounts-method Man page
variantType,SGVariantCounts-method Man page
variantType<-,SGVariants-method Man page
variantType,SGVariants-method Man page

Files

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

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