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SGSeq (version 1.6.2)

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

1.6.2

License

Artistic-2.0

Maintainer

Leonard Goldstein

Last Published

February 15th, 2017

Functions in SGSeq (1.6.2)

Transcript features

Example splice graph feature counts (annotation-based)

Identify splice variants from splice graph

annotateSGVariants

Annotate splice variants in terms of canonical events

Example splice variants (annotation-based)

convertToTxFeatures

Convert to TxFeatures object

sgvc_pred_from_bam

Example splice variant counts (predicted) from BAM files

predictExonsTerminal

Identify terminal exons

convertToSGFeatures

Convert transcript features to splice graph features

Obtain library information from BAM files

findOverlapsRanges

Modified findOverlaps function for IRanges, IRangesList objects

Plot read coverage and splice junction read counts

Example genomic region of interest

Splice graph segments

processTerminalExons

Process predicted terminal exons

predictTxFeaturesPerStrand

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

Filter predicted features

predictTxFeaturesPerSample

Identification of splice junctions and exons from BAM file

predictVariantEffects

Predict the effect of splice variants on protein-coding transcripts

getSGFeatureCounts

Compatible counts for splice graph features from BAM files

Example splice variant counts (predicted)

Ranges-based identification of splice junctions and exons

sgvc_ann_from_bam

Example splice variant counts (annotated) from BAM files

Example splice variant counts (annotated)

Example splice variants (predicted)

Accessing and replacing metadata columns

Compatible fragment counts for exons

Example transcript features (predicted)

Example transcripts

predictJunctions

Identify splice junctions

splicesiteOverlap

Compatible fragment counts for splice sites

SGFeatureCounts

Splice graph feature counts

analyzeVariants

Analysis of splice variants

Export to BED format

SGVariantCounts

Splice graph variant counts

getSGVariantCounts

Representative counts and frequency estimates for splice variants

Annotation with respect to transcript features

Splice graph variants

importTranscripts

Import transcripts from GFF file

predictExonsInternal

Identify internal exons

predictCandidatesInternal

Identify candidate internal exons

removeExonsIsolated

Remove exons with no flanking splice junctions

Example splice graph features (predicted)

analyzeFeatures

Analysis of splice graph features from BAM files

getSGFeatureCountsPerSample

Compatible fragment counts for splice graph features

mergeTxFeatures

Merge redundant features

Example splice graph feature counts (predicted)

Example splice graph features (annotation-based)

Plot splice graph and heatmap of expression values

Example sample information

Example transcript features (annotation-based)

makeSGFeatureCounts

Create SGFeatureCounts object

Splice graph features

predictTxFeatures

Splice junction and exon prediction from BAM files

Accessing and replacing assay data

makeVariantNames

Create interpretable splice variant names

junctionCompatible

Compatible fragment counts for splice junctions

predictCandidatesTerminal

Identify candidate terminal exons

Plot splice graph and heatmap of splice variant frequencies

plotSpliceGraph

Plot splice graph