Man pages for ldg21/SGSeq
Splice event prediction and quantification from RNA-seq data

analyzeFeaturesAnalysis of splice graph features from BAM files
analyzeVariantsAnalysis of splice variants
annotateAnnotation with respect to transcript features
annotateSGVariantsAnnotate splice variants in terms of canonical events
assaysAccessing and replacing assay data
convertToSGFeaturesConvert transcript features to splice graph features
convertToTxFeaturesConvert to TxFeatures object
exonCompatibleCompatible fragment counts for exons
exportFeaturesExport to BED format
filterFeaturesFilter predicted features
findOverlapsRangesModified 'findOverlaps' function for 'IRanges', 'IRangesList'...
findSGVariantsIdentify splice variants from splice graph
getBamInfoObtain library information from BAM files
getSGFeatureCountsCompatible counts for splice graph features from BAM files
getSGFeatureCountsPerSampleCompatible fragment counts for splice graph features
getSGVariantCountsRepresentative counts and frequency estimates for splice...
grExample genomic region of interest
importTranscriptsImport transcripts from GFF file
junctionCompatibleCompatible fragment counts for splice junctions
makeSGFeatureCountsCreate 'SGFeatureCounts' object
makeVariantNamesCreate interpretable splice variant names
mergeTxFeaturesMerge redundant features
plotCoveragePlot read coverage and splice junction read counts
plotFeaturesPlot splice graph and heatmap of expression values
plotSpliceGraphPlot splice graph
plotVariantsPlot splice graph and heatmap of splice variant frequencies
predictCandidatesInternalIdentify candidate internal exons
predictCandidatesTerminalIdentify candidate terminal exons
predictExonsInternalIdentify internal exons
predictExonsTerminalIdentify terminal exons
predictJunctionsIdentify splice junctions
predictSplicedRanges-based identification of splice junctions and exons
predictTxFeaturesSplice junction and exon prediction from BAM files
predictTxFeaturesPerSampleIdentification of splice junctions and exons from BAM file
predictTxFeaturesPerStrandIdentification of splice junctions and exons for a given...
predictVariantEffectsPredict the effect of splice variants on protein-coding...
processTerminalExonsProcess predicted terminal exons
removeExonsIsolatedRemove exons with no flanking splice junctions
sgf_annExample splice graph features (annotation-based)
sgfc_annExample splice graph feature counts (annotation-based)
sgfc_predExample splice graph feature counts (predicted)
SGFeatureCountsSplice graph feature counts
SGFeaturesSplice graph features
sgf_predExample splice graph features (predicted)
SGSegmentsSplice graph segments
sgv_annExample splice variants (annotation-based)
SGVariantCountsSplice graph variant counts
SGVariantsSplice graph variants
sgvc_annExample splice variant counts (annotated)
sgvc_ann_from_bamExample splice variant counts (annotated) from BAM files
sgvc_predExample splice variant counts (predicted)
sgvc_pred_from_bamExample splice variant counts (predicted) from BAM files
sgv_predExample splice variants (predicted)
siExample sample information
slotsAccessing and replacing metadata columns
splicesiteOverlapCompatible fragment counts for splice sites
txExample transcripts
txf_annExample transcript features (annotation-based)
TxFeaturesTranscript features
txf_predExample transcript features (predicted)
updateObjectUpdate object
ldg21/SGSeq documentation built on March 31, 2020, 2:29 p.m.