eb77e8d963dbdbff1897f636155f2871 *DESCRIPTION
71a315e88219cfad2204cd979b8f94b1 *LICENSE
dddb847c0c752be8d583cbaeebf9a885 *NAMESPACE
3be34ac70a2032a4139fc74ae1bdda8c *NEWS
ad161c40ef0fe3973694c5c6f7183c43 *R/AllGenerics-definitions.R
c51ba07e4a49d3df8ec707dbc63ecb4c *R/AllGenerics.R
4b1e824d10ec62417be72a4c62485339 *R/FRASER-package.R
69db903dca4249b2ade6593d3b7baf83 *R/Fraser-pipeline.R
e92518708191e5920056eae52cc3db6b *R/FraserDataSet-class.R
bfcfa7a2c4128b012d674cfb03218e70 *R/RcppExports.R
546710047fde47e626f9b0359e0a7281 *R/annotationOfRanges.R
b3cb343186881f7ce88852c1608bbd30 *R/autoencoder.R
68d2e7597b7bc88711842ee05ef2af13 *R/beta-binomial-testing.R
8e66bc1c8859ea9bdf9172c753450c38 *R/calculatePSIValue.R
712ed82a37a69ca95506e1813311f680 *R/countRNAseqData.R
2b101c7c6a2e09a25b4411e20bfd0f07 *R/example_functions.R
0693253d8286de54a5aacea60390f954 *R/filterExpression.R
8fbc318ba649410623e06ca91dbfeb8e *R/find_encoding_dimensions.R
9fcae10dfcb7a102cb9747223c5c2d81 *R/fitCorrectionMethods.R
92822b38816153eb659ecc3f494a5af5 *R/getNSetterFuns.R
9b282e843d1b019b3a812e813cd4b448 *R/getURLs.R
ac067ad75220a21906ada7c90ea57248 *R/helper-functions.R
fa1764144771ed2778243a6ecca3a545 *R/makeSimulatedDataset.R
fc5d678216f84a020a6ed184f5945a0e *R/mergeExternalData.R
5b0ccd4ade2493b2e7d26bd9ce0040cd *R/plotMethods.R
10c6498772e126c69824fa3fdbfde72f *R/pvalsNzscore.R
c2f96d422bafdfc31633e096e9c7a327 *R/resultAnnotations.R
f03a5c900175981ca4803a932ade24ed *R/saveHDF5Objects.R
965fbbe02aa58447af8319763a31f7de *R/updateD.R
53ff381d99a2ff9fd51668a902abdcc4 *R/updateE.R
e02f5006544657b9f3b6c97edc0cf8ee *R/updateRho.R
6cd808920ca536544e0a569a22bbbd71 *R/variables.R
6a28105513833bbc0574a1b4324c7cbc *R/zzz.R
334c7f0e62d81c27b35df1c289282052 *README.md
eb4675d213dd8b5a936eb4cd5d139f60 *build/vignette.rds
03c71ace3c8fcd46aad92cee6ba65ee3 *inst/CITATION
9f3976a5288650c7a9d19298c03a84df *inst/doc/FRASER.R
ec527ac3ec6036ca238894e926a4f6a5 *inst/doc/FRASER.Rnw
d6718f5e983ce1baba51f2b923e08a14 *inst/doc/FRASER.pdf
4e131fa3c6afbe106565ac2038e61b2c *inst/extdata/README.md
ec3e0ddedf82f939956780ce401ad090 *inst/extdata/bam/sample1.bam
4cd112124ffc648d49e4373e107adb48 *inst/extdata/bam/sample1.bam.bai
6f91c7028ed54a3387026e3792f1471b *inst/extdata/bam/sample2.bam
38bbf1f78551ae653075d2c0b4f98c67 *inst/extdata/bam/sample2.bam.bai
d83f74119d0c4ad9994506217c028c64 *inst/extdata/bam/sample3.bam
27c5d79cdd1f4c8e64d40040cf22e3be *inst/extdata/bam/sample3.bam.bai
24b982fd681020b1cf030b18a2f0f586 *inst/extdata/blacklist_regions/hg19-blacklist.v2.bed.gz
83fe6bf8187a64dee8079b80f75ba289 *inst/extdata/blacklist_regions/hg38-blacklist.v2.bed.gz
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e207059ade567f6b215741b3e319045a *inst/extdata/sampleTable_countTable.tsv
6be5dbf367b28f6d2353dfbafdc9ddf0 *inst/extdata/seqLevels_dict/hg19_NCBI2UCSC.tsv
cf4f3f528de24ca580052a1aa3995f77 *inst/extdata/seqLevels_dict/hg38_NCBI2UCSC.tsv
d5d5780c20ae70df45f27c6fcb80e3f6 *man/FRASER.Rd
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fcb807f44d7e123e1df01f46826aa2d8 *man/FraserDataSet.Rd
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0e1ca283a4015b91a1cd42f9079dde93 *man/assayNames-FraserDataSet-method.Rd
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be8e14907ca02e01d3be4cf3f915ae43 *man/calculatePSIValues.Rd
ae3855f7073ac8643301f98ff9e6a6a1 *man/countRNA.Rd
67375e0a93e651375185e05a3da828d6 *man/counts.Rd
c3d67c8115f840910db66c742162dddc *man/createTestFraserDataSet.Rd
5d1441da080db373f0750a8d58812198 *man/estimateBestQ.Rd
d472e9102490e9b5d53cce22c47880cb *man/fds-methods.Rd
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07be8a9b40ec925bd6ceb7ab3a5891e2 *man/fit.Rd
ca1cac89c4f0d65748ffadb0ed5e0a88 *man/getter_setter_functions.Rd
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66e59218940afdc491357909122fba29 *man/length-FraserDataSet-method.Rd
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8c5109dbe8ee77efa8d7eb1bc09cf036 *man/makeSimulatedFraserDataSet.Rd
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e292ca91e1988ac17a706ced79472520 *man/plotFunctions.Rd
4200531dc0de9dc13215d93b6e010916 *man/potentialImpactAnnotations.Rd
f83e93fdda647f4ff128140d087d3c3c *man/psiTypes.Rd
281b9b36f8e9fdf4e2d68028a9964b44 *man/results.Rd
e326721e1d7e81c902ad3d6f38abaa07 *man/subset.Rd
50b5423da082c03534ec4ede2348723e *src/Makevars
50b5423da082c03534ec4ede2348723e *src/Makevars.win
8196d2819a0a4cb7855a32f837378738 *src/RcppExports.cpp
264921296715da47097d6d94ef1d5731 *src/loss_n_gradient_functions.cpp
dd1a4797c401e31ac22a97c8eae167f3 *tests/testthat.R
5ae03d1ffafdd1b803e9edf23cc6628a *tests/testthat/gradient_loss_R.R
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108c4d86dc9128329d5f10996a900525 *tests/testthat/test_annotation_methods.R
ba58c16c843b76aae32bfacbc9ac4c03 *tests/testthat/test_betabinom.R
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c5f63a7736ea4a6c1c458ea17995aab0 *tests/testthat/test_estimateBestQ.R
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09171e95aba1a17d9433b5c9d60f527f *tests/testthat/test_plotJunctionDist.R
2843931800816c7ef78bd10490423114 *tests/testthat/test_plotSampleResults.R
b442d3eea7b66aee8a29fec020275c49 *tests/testthat/test_stats.R
9009d9f4035b77bb8b7c15af87c3e5f7 *tests/testthat/test_updateSeqlevelsStyle.R
d8441bfa7cd2856afaa86d72ce770632 *tests/testthat/test_utils.R
eae2d20ec764c90e06fea2b883bcda82 *tests/testthat/test_write_read_objects.R
ec527ac3ec6036ca238894e926a4f6a5 *vignettes/FRASER.Rnw
a2d634d378a38c0adf8e72bdc90b0503 *vignettes/FRASER_sketch.png
e33e74bc6942c4347f0b8918f44a67ab *vignettes/IntronJaccardIndex_sketch.png
0f3b4df3810c449c5a147ab48fdd1c0f *vignettes/bibliography.bib
