Files in GoekeLab/bambu
Context-Aware Transcript Quantification from Long Read RNA-Seq data
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.github/workflows/lint.yaml
.github/workflows/pr-commands.yaml
.github/workflows/test-coverage.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/RcppExports.R
R/bambu-extendAnnotations-utilityCombine.R
R/bambu-extendAnnotations-utilityExtend.R
R/bambu-extendAnnotations.R
R/bambu-processReads.R
R/bambu-processReads_scoreReadClasses.R
R/bambu-processReads_utilityConstructReadClasses.R
R/bambu-processReads_utilityCreateJunctionTables.R
R/bambu-processReads_utilityJunctionErrorCorrection.R
R/bambu-quantify.R
R/bambu-quantify_utilityFunctions.R
R/bambu.R
R/bambu_utilityFunctions.R
R/compareTranscripts.R
R/compareTranscripts_utilityFunctions.R
R/globals.R
R/plotBambu.R
R/plotBambu_utilityFunctions.R
R/prepareAnnotations.R
R/prepareAnnotations_utilityFunctions.R
R/prepareDataFromBam.R
R/readWrite.R
R/sysdata.rda
R/transcriptToGeneExpression.R
R/transcriptToGeneExpression_utilityFunctions.R
R/utility_spliceHelper_functions.R
README.md
data-raw/DATASET.R
docs/404.html
docs/LICENSE-text.html
docs/_config.yml
docs/articles/bambu.html
docs/articles/bambu_files/figure-html/unnamed-chunk-15-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-16-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-17-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-18-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-19-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-20-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-23-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-24-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-26-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-39-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-41-1.png
docs/articles/bambu_files/header-attrs-2.10/header-attrs.js
docs/articles/bambu_files/header-attrs-2.11/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/bambu.html
docs/reference/index.html
docs/reference/plotBambu.html
docs/reference/prepareAnnotations.html
docs/reference/readFromGTF.html
docs/reference/transcriptToGeneExpression.html
docs/reference/writeBambuOutput.html
docs/reference/writeToGTF.html
figures/bambu_design_highres.png
figures/plotGene.PNG
figures/plotHeatMap.PNG
figures/plotPCA.PNG
figures/plotTranscript.PNG
figures/transparent-bambu.png
inst/CITATION
inst/extdata/Homo_sapiens.GRCh38.91.annotations-txdb_chr9_1_1000000.sqlite
inst/extdata/Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf
inst/extdata/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa
inst/extdata/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa.fai
inst/extdata/SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam
inst/extdata/SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam.bai
inst/extdata/SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000_readClassSe.rds
inst/extdata/annotateSpliceOverlapByDist_testQuery.rds
inst/extdata/annotateSpliceOverlapByDist_testSubject.rds
inst/extdata/annotateSpliceOverlapsByDist_refoutput.rds
inst/extdata/annotationGranges_txdb2Grch38_91_chr9_1_1000000.rds
inst/extdata/annotationGranges_txdbGrch38_91_chr9_1_1000000.rds
inst/extdata/defaultModels.rds
inst/extdata/distanceToAnnotations_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/extendedAnnotationGranges_txdbGrch38_91_chr9_1_1000000.rds
inst/extdata/readClassesStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/readClassesUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/readGrgList_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/read_class_ME.model
inst/extdata/read_class_SE.model
inst/extdata/seIsoReCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seIsoReRef_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutputCombined2_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutputCombinedExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutputCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutputExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutput_denovo_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutput_distTable_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutput_lowMemoryMode_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutput_trackReads_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seReadClassBS_Stranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seReadClassStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seReadClass_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/standardJunctionModels_temp.txt
inst/extdata/xgb_model_splice_junction_correction.txt
inst/extdata/xgb_predictions_splice_junction_correction.txt
man/bambu.Rd
man/compareTranscripts.Rd
man/plotBambu.Rd
man/prepareAnnotations.Rd
man/readFromGTF.Rd
man/trainBambu.Rd
man/transcriptToGeneExpression.Rd
man/writeBambuOutput.Rd
man/writeToGTF.Rd
src/.gitignore
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/em.cpp
tests/testthat.R
tests/testthat/fixtures/.gitkeep
tests/testthat/test_assignGeneID.R
tests/testthat/test_bambu_arguments.R
tests/testthat/test_compareTranscripts.R
tests/testthat/test_isore.R
tests/testthat/test_plotBambu.R
tests/testthat/test_prepareAnnotations.R
tests/testthat/test_quant.R
tests/testthat/test_readWrite.R
tests/testthat/test_scoreRC.R
tests/testthat/test_transcriptToGeneExpression.R
tests/testthat/test_xgboost.R
vignettes/.gitignore
vignettes/bambu.Rmd
