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

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

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