Files in bambu
Reference-guided isoform reconstruction and quantification for long read RNA-Seq data
Dockerfile
LICENSE
NEWS
NAMESPACE
DESCRIPTION
README.md
tests/testthat.R
tests/testthat/test_readWrite.R
tests/testthat/test_plotBambu.R
tests/testthat/test_prepareAnnotations.R
tests/testthat/test_isore.R
tests/testthat/test_bambu.R
tests/testthat/test_transcriptToGeneExpression.R
figures/bambu_design_highres.png
figures/transparent-bambu.png
docs/bambu.html
docs/pkgdown.css
docs/docsearch.css
docs/authors.html
docs/pkgdown.yml
docs/bambu_0.2.0.pdf
docs/bootstrap-toc.js
docs/bambu_0.3.0.pdf
docs/404.html
docs/docsearch.js
docs/LICENSE-text.html
docs/pkgdown.js
docs/link.svg
docs/bootstrap-toc.css
docs/index.html
docs/articles/bambu.html
docs/articles/index.html
docs/articles/bambu_files/figure-html/unnamed-chunk-23-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-7-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-17-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-13-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-24-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-18-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-9-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-11-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-8-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-16-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-12-1.png
docs/articles/bambu_files/figure-html/unnamed-chunk-10-1.png
docs/reference/prepareAnnotations.html
docs/reference/bambu.html
docs/reference/readFromGTF.html
docs/reference/plot.bambu.html
docs/reference/writeToGTF.html
docs/reference/transcriptToGeneExpression.html
docs/reference/writeBambuOutput.html
docs/reference/index.html
docs/reference/prepareAnnotationsFromGTF.html
docs/reference/SEtoGTF.html
src/Makevars
src/em.cpp
src/Makevars.win
src/RcppExports.cpp
R/annotationFunctions.R
R/plotBambu.R
R/RcppExports.R
R/utility_annotation_functions.R
R/utility_bambu_functions.R
R/utility_rcContruct_functions.R
R/utility_spliceHelper_functions.R
R/bambu.R
R/prepareBam.R
R/sysdata.rda
R/readWrite.R
R/utiltiy_quant_functions.R
R/globals.R
R/utility_discovery_functions.R
R/utility_general_functions.R
R/utility_plot_functions.R
R/utility_junctionCorrection_functions.R
R/transcriptToGeneExpression.R
man/writeBambuOutput.Rd
man/bambu.Rd
man/writeToGTF.Rd
man/plotBambu.Rd
man/readFromGTF.Rd
man/transcriptToGeneExpression.Rd
man/prepareAnnotations.Rd
inst/citation
inst/extdata/seIsoReCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seReadClassStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/annotationGranges_txdbGrch38_91_chr9_1_1000000.rds
inst/extdata/seOutputCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/extendedAnnotationGranges_txdbGrch38_91_chr9_1_1000000.rds
inst/extdata/seIsoReRef_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf
inst/extdata/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa.fai
inst/extdata/seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/readGrgList_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
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/Homo_sapiens.GRCh38.91.annotations-txdb_chr9_1_1000000.sqlite
inst/extdata/seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seOutputCombinedExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seReadClassBS_Stranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa
inst/extdata/seOutputExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/extdata/seReadClass_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
inst/doc/bambu.html
inst/doc/bambu.R
inst/doc/bambu.Rmd
data-raw/DATASET.R
build/vignette.rds
vignettes/bambu.Rmd
