Files in ldg21/SGSeq

Splice event prediction and quantification from RNA-seq data

R/annotation.R R/classes.R R/convert.R R/counts.R R/data.R R/features-filter.R R/features-merge.R R/features-prediction.R R/graphs.R R/main.R R/misc.R R/overlaps.R R/plots.R R/sequences.R R/slots-generics.R R/slots-methods.R inst/scripts/createExampleData.R inst/unitTests/test_analyzeFeatures.R inst/unitTests/test_analyzeVariants.R inst/unitTests/test_annotate.R inst/unitTests/test_classes.R inst/unitTests/test_convertToSGFeatures.R inst/unitTests/test_convertToTxFeatures.R inst/unitTests/test_findSGVariants.R inst/unitTests/test_getBamInfo.R inst/unitTests/test_getSGFeatureCounts.R inst/unitTests/test_getSGVariantCounts.R inst/unitTests/test_mergeTxFeatures.R inst/unitTests/test_predictTxFeatures.R inst/unitTests/test_predictVariantEffects.R man/SGFeatureCounts.Rd man/SGFeatures.Rd man/SGSegments.Rd man/SGVariantCounts.Rd man/SGVariants.Rd man/TxFeatures.Rd man/analyzeFeatures.Rd man/analyzeVariants.Rd man/annotate.Rd man/annotateSGVariants.Rd man/assays.Rd man/convertToSGFeatures.Rd man/convertToTxFeatures.Rd man/exonCompatible.Rd man/exportFeatures.Rd man/filterFeatures.Rd man/findOverlapsRanges.Rd man/findSGVariants.Rd man/getBamInfo.Rd man/getSGFeatureCounts.Rd man/getSGFeatureCountsPerSample.Rd man/getSGVariantCounts.Rd man/gr.Rd man/importTranscripts.Rd man/junctionCompatible.Rd man/makeSGFeatureCounts.Rd man/makeVariantNames.Rd man/mergeTxFeatures.Rd man/plotCoverage.Rd man/plotFeatures.Rd man/plotSpliceGraph.Rd man/plotVariants.Rd man/predictCandidatesInternal.Rd man/predictCandidatesTerminal.Rd man/predictExonsInternal.Rd man/predictExonsTerminal.Rd man/predictJunctions.Rd man/predictSpliced.Rd man/predictTxFeatures.Rd man/predictTxFeaturesPerSample.Rd man/predictTxFeaturesPerStrand.Rd man/predictVariantEffects.Rd man/processTerminalExons.Rd man/removeExonsIsolated.Rd man/sgf_ann.Rd man/sgf_pred.Rd man/sgfc_ann.Rd man/sgfc_pred.Rd man/sgv_ann.Rd man/sgv_pred.Rd man/sgvc_ann.Rd man/sgvc_ann_from_bam.Rd man/sgvc_pred.Rd man/sgvc_pred_from_bam.Rd man/si.Rd man/slots.Rd man/splicesiteOverlap.Rd man/tx.Rd man/txf_ann.Rd man/txf_pred.Rd man/updateObject.Rd tests/runTests.R vignettes/SGSeq.Rmd vignettes/classes.pdf