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SGSeq (version 1.6.5)

Splice event prediction and quantification from RNA-seq data

Description

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.

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Version

Version

1.6.5

License

Artistic-2.0

Maintainer

Leonard Goldstein

Last Published

February 15th, 2017

Functions in SGSeq (1.6.5)

convertToTxFeatures

Convert to TxFeatures object

Accessing and replacing assay data

annotateSGVariants

Annotate splice variants in terms of canonical events

Filter predicted features

convertToSGFeatures

Convert transcript features to splice graph features

Annotation with respect to transcript features

Export to BED format

analyzeFeatures

Analysis of splice graph features from BAM files

analyzeVariants

Analysis of splice variants

Compatible fragment counts for exons

getSGFeatureCountsPerSample

Compatible fragment counts for splice graph features

getSGVariantCounts

Representative counts and frequency estimates for splice variants

findOverlapsRanges

Modified findOverlaps function for IRanges, IRangesList objects

Identify splice variants from splice graph

getSGFeatureCounts

Compatible counts for splice graph features from BAM files

Obtain library information from BAM files

importTranscripts

Import transcripts from GFF file

Example genomic region of interest

junctionCompatible

Compatible fragment counts for splice junctions

makeSGFeatureCounts

Create SGFeatureCounts object

Plot read coverage and splice junction read counts

Plot splice graph and heatmap of expression values

predictTxFeaturesPerStrand

Identification of splice junctions and exons for a given chromosome and strand

Example splice graph feature counts (annotation-based)

predictVariantEffects

Predict the effect of splice variants on protein-coding transcripts

Example splice graph feature counts (predicted)

predictJunctions

Identify splice junctions

Ranges-based identification of splice junctions and exons

Splice graph segments

Example splice variants (annotation-based)

Example transcripts

Example transcript features (annotation-based)

plotSpliceGraph

Plot splice graph

Plot splice graph and heatmap of splice variant frequencies

Example sample information

Example splice variant counts (predicted)

Example splice graph features (annotation-based)

Example splice graph features (predicted)

SGFeatureCounts

Splice graph feature counts

Splice graph features

predictExonsInternal

Identify internal exons

Splice graph variants

Accessing and replacing metadata columns

splicesiteOverlap

Compatible fragment counts for splice sites

sgvc_ann_from_bam

Example splice variant counts (annotated) from BAM files

predictExonsTerminal

Identify terminal exons

predictTxFeatures

Splice junction and exon prediction from BAM files

makeVariantNames

Create interpretable splice variant names

mergeTxFeatures

Merge redundant features

predictTxFeaturesPerSample

Identification of splice junctions and exons from BAM file

SGVariantCounts

Splice graph variant counts

Example splice variant counts (annotated)

Example splice variants (predicted)

sgvc_pred_from_bam

Example splice variant counts (predicted) from BAM files

predictCandidatesInternal

Identify candidate internal exons

predictCandidatesTerminal

Identify candidate terminal exons

processTerminalExons

Process predicted terminal exons

removeExonsIsolated

Remove exons with no flanking splice junctions

Example transcript features (predicted)

Transcript features