Files in cancer-genomics/trellis
Somatic structural variant analysis
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/.DS_Store
R/AllGenerics.R
R/Amplicon-class.R
R/DNAcopy-class.R
R/Deletion-class.R
R/DeletionList-class.R
R/DeletionParam-class.R
R/ExonSubset-class.R
R/GAlignmentPairs-utils.R
R/GRanges-utils.R
R/Preprocess-class.R
R/Rearrangement-class.R
R/RearrangementList-class.R
R/RearrangementParams-class.R
R/RearrangmentParams-class.R
R/SegmentParam-class.R
R/Transcripts-class.R
R/acf.R
R/alignment-utils.R
R/amplicon-utils.R
R/baf-utils.R
R/blat-utils.R
R/copynumber-methods.R
R/data-utils.R
R/data.R
R/deletion-utils.R
R/fasta-utils.R
R/functions.R
R/fusion-utils.R
R/galignment-utils.R
R/germlineOutliers.R
R/help.R
R/improper-methods.R
R/listCNVs.R
R/listGenomeFilters.R
R/preprocess-utils.R
R/read_pairs.R
R/rear_reads.R
R/rearlist-utils.R
R/rearrangement-utils.R
R/recurrent.R
R/segment.R
R/seqinfo-utils.R
R/uniprot.R
README
contributing.md
data-derived/axis_limits.R
data-raw/amplicon_graph.R
data-raw/bamviews.R
data-raw/cgov44t_deletions.R
data-raw/cgov44t_segments.R
data-raw/complex_rearrangement.R
data-raw/data-raw.org
data-raw/deletion.R
data-raw/functions.R
data-raw/ikzf2.R
data-raw/rear_list.R
data-raw/rearlist.R
data-raw/rearrangements_cgov44t.R
data-raw/rlist_with_invalid_split_reads.R
data-raw/segmentation.R
data-raw/sequence_tags.R
data-raw/split_reads_cgov44t.R
data-raw/split_reads_cgov7t.R
data-raw/unmapped_blat_oralcleft.R
data-raw/yap1-mamml_rear.R
data/amplicons.rda
data/deletions.rda
data/pdata.rda
data/rear_cds.rda
data/rear_cgov7t.rda
data/rear_list.rda
data/rlist.rda
data/segments.rda
data/tags.rda
inst/extdata/chr6-12_rear.rds
inst/extdata/rearrangement_types.csv
inst/extdata/rlist_cgov30t1.rds
man/AmpliconGraph-class.Rd
man/AmpliconGraph-constructor.Rd
man/ClippedTranscripts-class.Rd
man/DNAcopy-methods.Rd
man/DeletionList-methods.Rd
man/DeletionParam-class.Rd
man/ExonSubset-class.Rd
man/GAlignmentPairs.Rd
man/PreprocessViews2-class.Rd
man/PreprocessViews2-coercion.Rd
man/Rearrangement-class.Rd
man/RearrangementList-class.Rd
man/RearrangementParams-class.Rd
man/SegmentParam-class.Rd
man/StructuralVariant-class.Rd
man/Transcripts-class.Rd
man/TranscriptsFusion-class.Rd
man/aa_granges.Rd
man/aberrantSep.Rd
man/acf2.Rd
man/addFocalDupsFlankingAmplicon.Rd
man/alignment-flags.Rd
man/ampliconParams.Rd
man/amplicon_graph.Rd
man/amplicons-data.Rd
man/annotateBlatRecords.Rd
man/annotateRecurrent.Rd
man/assays-PreprocessViews2-method.Rd
man/binFragments.Rd
man/binGCCorrect.Rd
man/binMedians.Rd
man/binNormalize.Rd
man/binnedCounts.Rd
man/blatScores.Rd
man/blat_unmapped.Rd
man/calls-method.Rd
man/cbs2granges.Rd
man/chromosome-methods.Rd
man/clip.Rd
man/codingJunctions.Rd
man/copynumber-methods.Rd
man/countParam.Rd
man/countReads2.Rd
man/deletion.Rd
man/deletion_call.Rd
man/deletions.Rd
man/deletions2.Rd
man/duplicatedGAlignmentPairs.Rd
man/expandGRanges.Rd
man/fasta.Rd
man/fasta_unmapped.Rd
man/filterBy-methods.Rd
man/filterGermlineRear.Rd
man/filterGermlineRearList.Rd
man/filterPairedReads.Rd
man/filterRear.Rd
man/filterRearExperiment.Rd
man/filterRearrangementList.Rd
man/findCandidates2.Rd
man/fiveTo3List.Rd
man/fiveTo3Prime.Rd
man/focalAmpliconDupRanges.Rd
man/fractionLinkingTags.Rd
man/fullTranscripts.Rd
man/fuse-methods.Rd
man/fuseCDS_Rlist.Rd
man/fusionList.Rd
man/fusionTable.Rd
man/fusionTable2.Rd
man/ga2gr.Rd
man/germlineFilters.Rd
man/germlineOutliers.Rd
man/getCDS.Rd
man/getImproperAlignmentPairs.Rd
man/getProperAlignmentPairs.Rd
man/getSequenceOfReads-methods.Rd
man/get_improper_readpairs.Rd
man/get_readpairs.Rd
man/get_readpairs2.Rd
man/ggRearrange.Rd
man/granges_copynumber.Rd
man/groupAmplicons.Rd
man/groupedVariant-method.Rd
man/improper-methods.Rd
man/inFrameFusions.Rd
man/inFrameList.Rd
man/inFrameNoStop.Rd
man/indexRanges-method.Rd
man/indexing-methods.Rd
man/intOverWidth.Rd
man/intersectionAligned.Rd
man/isComplex.Rd
man/isDuplicate.Rd
man/isNotGermline.Rd
man/is_valid_splits.Rd
man/joinNearGRanges.Rd
man/linkedBins-methods.Rd
man/linkedTo.Rd
man/listCNVs.Rd
man/listDeletions.Rd
man/listFusionData.Rd
man/listGenomeFilters.Rd
man/loadTx.Rd
man/loadTxDb.Rd
man/loadTxdbTranscripts.Rd
man/makeAGraph.Rd
man/modalRearrangement.Rd
man/noPrematureStop.Rd
man/numberImproper.Rd
man/numberLinkingRP-methods.Rd
man/numberOverlappingDeletions.Rd
man/organizeReads.Rd
man/organizeReferenceByFrame.Rd
man/partitionAASequence.Rd
man/paths.Rd
man/pdata.Rd
man/percentRearrangement.Rd
man/preprocessData.Rd
man/promoterCDS.Rd
man/proper-methods.Rd
man/properReadPairs.Rd
man/rFilters.Rd
man/rdsId.Rd
man/readBlat.Rd
man/readPairsAsSegments.Rd
man/readPairsNearVariant.Rd
man/rearDataFrame.Rd
man/rearDataFrameList.Rd
man/rear_cds-data.Rd
man/rear_cgov7t.Rd
man/rear_list-data.Rd
man/rearrangedReadList.Rd
man/rearrangedReads.Rd
man/rearrangementData.Rd
man/rearrangementType.Rd
man/rearrangement_list.Rd
man/recurrentDeletions.Rd
man/recurrentDrivers.Rd
man/reduceGenomeFilters.Rd
man/referenceProtein.Rd
man/removeAmbiguousAln.Rd
man/rpSupportedDeletions.Rd
man/sapply-methods.Rd
man/scale_x_mb.Rd
man/segmentBins.Rd
man/segmentExperiment.Rd
man/segments.Rd
man/seqJunctionNearTx.Rd
man/seqJunctionsInferredByPairedTags2.Rd
man/seqJunctions_Rlist.Rd
man/setScale-method.Rd
man/sortByRead1.Rd
man/splitReads.Rd
man/svAF.Rd
man/sv_amplicon_exp.Rd
man/sv_amplicons.Rd
man/sv_amplicons2.Rd
man/sv_deletions.Rd
man/tag_sequenceExperiment.Rd
man/tags-methods.Rd
man/thinProperPairs.Rd
man/thinReadPairs.Rd
man/threshold.Rd
man/totalWidth.Rd
man/transcript-accessors.Rd
man/translateCDS.Rd
man/trellis.Rd
man/tumorProtein.Rd
man/type_rearrangement.Rd
man/uncouple.Rd
man/uniprotFeatures.Rd
man/unmapped_read.Rd
man/validFusions.Rd
man/variant-methods.Rd
tests/.DS_Store
tests/testthat.R
tests/testthat/.Rapp.history
tests/testthat/deletion-4500T3.R
tests/testthat/temp.rds
tests/testthat/temp_reviseEachJunction_args.rds
tests/testthat/temp_updateImproperIndex2_args.rds
tests/testthat/test_AmpliconGraph.R
tests/testthat/test_CNAObject.R
tests/testthat/test_DeletionList.R
tests/testthat/test_DeletionParam.R
tests/testthat/test_ExonSubset.R
tests/testthat/test_Rearrangement.R
tests/testthat/test_RearrangementList.R
tests/testthat/test_RearrangementParams.R
tests/testthat/test_StructuralVariant.R
tests/testthat/test_Transcript.R
tests/testthat/test_addFocalDupsFlankingAmplicon.R
tests/testthat/test_amplicon_regressions.R
tests/testthat/test_annotation.R
tests/testthat/test_axis_limits.R
tests/testthat/test_barcodes.R
tests/testthat/test_binCounts.R
tests/testthat/test_binFragments.R
tests/testthat/test_binGCCorrect.R
tests/testthat/test_binNormalize.R
tests/testthat/test_blatScores.R
tests/testthat/test_candidate_regressions.R
tests/testthat/test_chromosome.R
tests/testthat/test_complex_rearrangement.R
tests/testthat/test_deletion_regressions.R
tests/testthat/test_duplicatedGAlignmentPairs.R
tests/testthat/test_expandGRanges.R
tests/testthat/test_filter_regressions.R
tests/testthat/test_fiveTo3prime.R
tests/testthat/test_focalAmpDupRanges.R
tests/testthat/test_fusionTable2.R
tests/testthat/test_fusion_regression.R
tests/testthat/test_genomeFilters.R
tests/testthat/test_getImproperAlignmentPairs.R
tests/testthat/test_getSequenceOfReads.R
tests/testthat/test_ggRearrange.R
tests/testthat/test_ikzf2.R
tests/testthat/test_improperAlignmentParams.R
tests/testthat/test_inframe.R
tests/testthat/test_intOverWidth.R
tests/testthat/test_invalid_split_reads.R
tests/testthat/test_joinNeargRanges.R
tests/testthat/test_linkDuplicatedRanges.R
tests/testthat/test_organizeReads.R
tests/testthat/test_ovarian_cellLines.R
tests/testthat/test_overlappingHemizygous.R
tests/testthat/test_promoter.R
tests/testthat/test_properReadPairs.R
tests/testthat/test_protein_domains.R
tests/testthat/test_rearrangedReads.R
tests/testthat/test_recurrentDeletions.R
tests/testthat/test_reviseEachJunction.R
tests/testthat/test_segmentation.R
tests/testthat/test_seqinfo.R
tests/testthat/test_split_reads.R
tests/testthat/test_vaf.R
tests/testthat/test_vignette_deletion.R
tests/testthat/test_writeImproperAlignments.R
tests/testthat/test_writeToFasta.R
vignettes/trellis.Rmd
