94bf45e41b602f62cae0263edac2c7ab *DESCRIPTION
1ebbd3e34237af26da5dc08a4e440464 *LICENSE
c651ac305408b99df185c05a23607d4b *NAMESPACE
2372455ac42d8fde78ba9be6a79187d0 *NEWS
685afec3fbdecfb14a208c40db9aadbf *R/RcppExports.R
08f8b431c1945336619a4e41c70861fa *R/bambu-extendAnnotations-utilityCombine.R
372b5c8e40c69e451c318672464f9aeb *R/bambu-extendAnnotations-utilityExtend.R
7b10ce460dd4e4661c691186f956526d *R/bambu-extendAnnotations.R
980435334493bc7ec3c394b5e5123cf8 *R/bambu-processReads.R
7c996b941a1994c70be89b34b54d3297 *R/bambu-processReads_scoreReadClasses.R
debabf9c3fac6cfbd4917f0150ecc81f *R/bambu-processReads_utilityConstructReadClasses.R
4bf1b17a238965cfcf2a8cfaf50f4b34 *R/bambu-processReads_utilityCreateJunctionTables.R
9dd5b775bc92502adb4c235366c91a04 *R/bambu-processReads_utilityJunctionErrorCorrection.R
15885df416db7070c92b67bc31d04348 *R/bambu-quantify.R
39cadbc9168d3c640668821ce2f8bbc7 *R/bambu-quantify_utilityFunctions.R
d744c67f07d3b00c2a25a7dbd3772ffd *R/bambu.R
93081f687cd9e26c77bc7049da7b0ad8 *R/bambu_utilityFunctions.R
0e70efc0951fc8f1b6650b8d75656c6a *R/compareTranscripts.R
33f67998e860534385df6ba641adadca *R/compareTranscripts_utilityFunctions.R
d79c22dcc309fc744e39b157eef161c0 *R/globals.R
757bce9837fa5148f227d8482c351111 *R/plotBambu.R
4a6c43f2650bbc63fecc36bc14caaef9 *R/plotBambu_utilityFunctions.R
4e83cfeac51864ce8573a06b8804ec3d *R/prepareAnnotations.R
9d146df9ed4bb14a93fdfbdc79a8c59f *R/prepareAnnotations_utilityFunctions.R
f6097bc534455901d4abc5e0ed0b2ee0 *R/prepareDataFromBam.R
0bfce3bede66bdd16ea2610a86127207 *R/readWrite.R
1a1bee48b6158159a50caaaa03d7d75d *R/sysdata.rda
019d4f308fe71b4bf154092ec4519e50 *R/transcriptToGeneExpression.R
737993ba8394d080ed5d11a76a622a42 *R/transcriptToGeneExpression_utilityFunctions.R
28bc757fb5cd33d1fda00fe013128749 *R/utility_spliceHelper_functions.R
48f2dbfa197ab0e57842537605d5fff1 *README.md
8973938fee029a1080cc988ff4966d9e *build/vignette.rds
80ccba2f4ca5f1cd76e449a51d0d4fd2 *data-raw/DATASET.R
daf53b8ef4cff21116079613cd636ca8 *figures/bambu_design_highres.png
5b99abf45cff9c12482251c766d507de *figures/plotGene.PNG
da16f1be47b877718c0844487e111d76 *figures/plotHeatMap.PNG
e34f4d3ababf00eac04d0d2e5fe03e44 *figures/plotPCA.PNG
7a4cb4d8e72f5cceca0fa2c58cb275a2 *figures/plotTranscript.PNG
fcdd089086af6dbe54d7ab73e2bce365 *figures/transparent-bambu.png
fd79a73a3aadfe65d4d77ba52b75cda4 *inst/CITATION
ebb7d3fd5ec8e755527a3bec06fb1efc *inst/doc/bambu.R
0e93ae067b5b73c9df8f1e659fa5d181 *inst/doc/bambu.Rmd
728262a37a8655698e0f98b4df6b297b *inst/doc/bambu.html
aa95917805efcfe9bc76e306208fec1a *inst/extdata/Homo_sapiens.GRCh38.91.annotations-txdb_chr9_1_1000000.sqlite
123638b7a424504dabf19dade96a8868 *inst/extdata/Homo_sapiens.GRCh38.91_chr9_1_1000000.gtf
378f0bb57e44dcf91cd44d879da21bd5 *inst/extdata/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa
2653234c35fbb855d298bf75233e4962 *inst/extdata/Homo_sapiens.GRCh38.dna_sm.primary_assembly_chr9_1_1000000.fa.fai
a9d06b3b5d44984714a8be7c5a2ba7c0 *inst/extdata/SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam
d016a5e09abcc432c87abe2ffe502662 *inst/extdata/SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.bam.bai
1e0b9d85e569271cd05ff2f37ba5c293 *inst/extdata/SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000_readClassSe.rds
f63e9e0da4939329f1a49e9956885550 *inst/extdata/annotateSpliceOverlapByDist_testQuery.rds
02a8ad14f3e6086aed9923bfb2fab191 *inst/extdata/annotateSpliceOverlapByDist_testSubject.rds
13a80407a57f71343245bec367a73b39 *inst/extdata/annotateSpliceOverlapsByDist_refoutput.rds
ee23de13c8071eb314df4ae49c43b818 *inst/extdata/annotationGranges_txdb2Grch38_91_chr9_1_1000000.rds
bb13aaac275fde70e2f68238b41fc966 *inst/extdata/annotationGranges_txdbGrch38_91_chr9_1_1000000.rds
b08742c210251be954952e2fce1990ca *inst/extdata/defaultModels.rds
fd6041f096c58ab238bda428416f155c *inst/extdata/distanceToAnnotations_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
916c6a26d96a75dee56694fb6b952a2c *inst/extdata/extendedAnnotationGranges_txdbGrch38_91_chr9_1_1000000.rds
adacbc5861eccdb7641d1a7a261907b0 *inst/extdata/readClassesStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
a8e0274d4c91d2528abee7fb94c85985 *inst/extdata/readClassesUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
c75abfae5702007c478e889e3a0c8a10 *inst/extdata/readGrgList_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
ddec6a66f7643a7b59bec9f8419bcc1e *inst/extdata/read_class_ME.model
23ba1c31131c9ccc591f2bca3d5e67be *inst/extdata/read_class_SE.model
56474106510b07313158241d98e2951d *inst/extdata/seIsoReCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
823b71e2129fc75c36836839b70d6f3d *inst/extdata/seIsoReRef_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
a3c920614df5529c3dcf73cf94671c07 *inst/extdata/seOutputCombined2_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
25141f7792c42f39e321da406b1a331b *inst/extdata/seOutputCombinedExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
99fac3b4254cca1240270774506779e6 *inst/extdata/seOutputCombined_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
f7ac17a361e703e91c89ec04f82a54bd *inst/extdata/seOutputExtended_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
1e7eec2e6863902fe42c63d5c420b14f *inst/extdata/seOutput_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
656d9870557e5857388c36b8d1dd96a1 *inst/extdata/seOutput_denovo_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
1dd3536a540c8059b90eebf59eea7583 *inst/extdata/seOutput_distTable_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
8810a4f1a5daa33819c43554450b0977 *inst/extdata/seOutput_lowMemoryMode_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
fdbc1c7f9a788fd83fac7f097857e8c6 *inst/extdata/seOutput_trackReads_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
3810f62ddeac4f4edd2fd2f0f5f1136f *inst/extdata/seReadClassBS_Stranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
3c5b2d02ea85fddac083e20cf36a5e30 *inst/extdata/seReadClassStranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
8ab4b5c2ee06c4696c6d872c4c182019 *inst/extdata/seReadClassUnstranded_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
fb21a9fc769f40213b39d5c5c8fd2dbf *inst/extdata/seReadClass_SGNex_A549_directRNA_replicate5_run1_chr9_1_1000000.rds
aad0f4043a95b6c32f54c17cf3204c24 *inst/extdata/standardJunctionModels_temp.txt
f2e58e77f6aa6156e05a673105963e66 *inst/extdata/xgb_model_splice_junction_correction.txt
9abef86ffb62aaa349eb37ab3fb7db1c *inst/extdata/xgb_predictions_splice_junction_correction.txt
7b693e5ea948fbd307610839a322cd6b *man/bambu.Rd
5e16b4a7f6196c7bc738fa3e46c930ef *man/compareTranscripts.Rd
447e7a7afca665b0e3e6d7bf38b85a8b *man/plotBambu.Rd
d14d94da1612d8341d8595a2486ae1c0 *man/prepareAnnotations.Rd
7ee5835789eb256cc4b7eaa556fbddb7 *man/readFromGTF.Rd
6aeb415f5c93d0a45f56e2f27820fba7 *man/trainBambu.Rd
32ef17e2d28ad67a505014004d4e1586 *man/transcriptToGeneExpression.Rd
294617711cb1912e93f54ab2d6cefa6d *man/writeBambuOutput.Rd
13b3d4c7cf91fa23663351d126133b1c *man/writeToGTF.Rd
d6c2de6b15a61cc3d95c8e0195bfe36a *src/Makevars
33de3ee9a86ca50273bd2aea4658b14b *src/Makevars.win
e70895208619c0adc6c507db6344601f *src/RcppExports.cpp
05d3d105a39a4f580ad01fd79beccc92 *src/em.cpp
1dae1ddbcc635c0987dad2cf8e7c3b39 *tests/testthat.R
a7cfe954bca15fef516c059eaf6a279a *tests/testthat/test_assignGeneID.R
0d89077b4135001b1ea26420eecddcc7 *tests/testthat/test_bambu_arguments.R
32036f8f37745ece782e95ad31966c76 *tests/testthat/test_compareTranscripts.R
8654b7865be391db397330b955cd16e9 *tests/testthat/test_isore.R
e592ecc7dfcd619c089bc3fff260da22 *tests/testthat/test_plotBambu.R
59f3919b25c65a2a7b217a30e8e35d2c *tests/testthat/test_prepareAnnotations.R
430b37fe6ffb2bb8a9127fd9cc3d93d3 *tests/testthat/test_quant.R
6dbf45d7f0a73da43f0a83bedb7f843b *tests/testthat/test_readWrite.R
70681af453866502a5a05fb3019ae8e9 *tests/testthat/test_scoreRC.R
668490315e6fabaa569e49ebacb60deb *tests/testthat/test_transcriptToGeneExpression.R
ad63c2fb5e2582b172c2f00b41c2a5ce *tests/testthat/test_xgboost.R
0e93ae067b5b73c9df8f1e659fa5d181 *vignettes/bambu.Rmd
