Files in ldg21/SGSeq
Splice event prediction and quantification from RNA-seq data
DESCRIPTION
NAMESPACE
NEWS
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
data/gr.rda
data/sgf_ann.rda
data/sgf_pred.rda
data/sgfc_ann.rda
data/sgfc_pred.rda
data/sgv_ann.rda
data/sgv_pred.rda
data/sgvc_ann.rda
data/sgvc_ann_from_bam.rda
data/sgvc_pred.rda
data/sgvc_pred_from_bam.rda
data/si.rda
data/tx.rda
data/txf_ann.rda
data/txf_pred.rda
inst/CITATION
inst/extdata/bams/N1.bam
inst/extdata/bams/N1.bam.bai
inst/extdata/bams/N2.bam
inst/extdata/bams/N2.bam.bai
inst/extdata/bams/N3.bam
inst/extdata/bams/N3.bam.bai
inst/extdata/bams/N4.bam
inst/extdata/bams/N4.bam.bai
inst/extdata/bams/T1.bam
inst/extdata/bams/T1.bam.bai
inst/extdata/bams/T2.bam
inst/extdata/bams/T2.bam.bai
inst/extdata/bams/T3.bam
inst/extdata/bams/T3.bam.bai
inst/extdata/bams/T4.bam
inst/extdata/bams/T4.bam.bai
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/SGSeq.bib
vignettes/classes.pdf
vignettes/classes.png
