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.

Author
Leonard Goldstein
Date of publication
None
Maintainer
Leonard Goldstein <goldstel@gene.com>
License
Artistic-2.0
Version
1.8.1

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

Files in this package

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