645585ad5aced900e4b66f7ab2315aa9 *DESCRIPTION
6621d5f58a1e621e537098fb6d553ebb *NAMESPACE
a0fddb94813c5ed2c6f607d24b436efd *NEWS
092f18d20564e6628c8eff842a621fb1 *R/annotation.R
55cd7fb241410268fd51e651b78b12e8 *R/classes.R
ebbd303f3458de0240ce08f025084e59 *R/convert.R
049062ada3d1b9d10b474a5965f1c182 *R/counts.R
463367049f605ac5ed74c989bf0e5dac *R/data.R
438009e01ab7e5d88ae6e64db3c34106 *R/features-filter.R
e775ee1ab0cfe9de085dab1dc293a610 *R/features-merge.R
da660660034d3fabfb2ad6f803b36515 *R/features-prediction.R
9f671cdba87f21e3d8067ad0cf5d4a20 *R/graphs.R
e746e6705e5c0d317a78afbe4e864d27 *R/main.R
4c32527dd5a03318423e1f76d2fd6765 *R/misc.R
59f79eccdc546e23d754d87296f1f056 *R/overlaps.R
80da73d99afccfd6897d602cd24c2b4a *R/plots.R
46413ac2dbb7f669dbdc18270d303c0f *R/sequences.R
278848884364b94b56d9a18493546469 *R/slots-generics.R
6db56f4307d5f8ae14ec1d20c1f42cd1 *R/slots-methods.R
c64e291b95b86c293bfc001882a0d4fe *build/vignette.rds
d07020009fd005e602ca3479141072f7 *data/gr.rda
2a8a6beed87991caa5cbc16368c3c387 *data/sgf_ann.rda
5478dd19068388d0a72cd3a49b5d2030 *data/sgf_pred.rda
145e9ea1f875c4a537fc9db70e9fbf6c *data/sgfc_ann.rda
1ee71e6e2e3abd16b5a10cf4ac63e648 *data/sgfc_pred.rda
6a4ef900c17decd3d806fd8fbe3c2139 *data/sgv_ann.rda
3a5af35e058e36d89148772d1bc19121 *data/sgv_pred.rda
b4d81ce76fe89db9b98657fbabde4fef *data/sgvc_ann.rda
0ba99e2a6bf7e78d3931b281fc46bef0 *data/sgvc_ann_from_bam.rda
177ff48dd3eeba21b07231c7097aa538 *data/sgvc_pred.rda
4ab10d8da03636d14fd3cb694f43dadd *data/sgvc_pred_from_bam.rda
c16f6e568409993470840a62bde5bce5 *data/si.rda
bf8011395a39d8a71366ffd457dd8bf8 *data/tx.rda
000563cf3823f3506b8920cf82bb414d *data/txf_ann.rda
05bef728ed9786e38809d288411041c1 *data/txf_pred.rda
c3bde156c0761d9578badd79a0161031 *inst/CITATION
4c5891cdcb837d077f12866293a11d85 *inst/doc/SGSeq.R
a1bedcc062dbe7d53c768689aa8c88eb *inst/doc/SGSeq.Rmd
9c0f54abf3ac90c82033d6fed83e1dbc *inst/doc/SGSeq.html
f635a290f6dd7bd6a571a748b9b4ce2d *inst/extdata/bams/N1.bam
10e437ecd83a1648f6feb28efd666a3d *inst/extdata/bams/N1.bam.bai
6ae387d023817532da8ab3273731c6b7 *inst/extdata/bams/N2.bam
7bc7623be9eb5b52f7d272b1e54d7c1f *inst/extdata/bams/N2.bam.bai
e07e5bf79859b2028cb402c079577316 *inst/extdata/bams/N3.bam
20cd985ef7ffa218da184f187ce50dea *inst/extdata/bams/N3.bam.bai
b0a8a2796e4cd67d1c5231481dc298f7 *inst/extdata/bams/N4.bam
c14641aca82d7b303f9ab448ce5b4f2e *inst/extdata/bams/N4.bam.bai
dab9dc6d74c1e618b960baa0148740af *inst/extdata/bams/T1.bam
f1bd4bdf90f83ca520ab1fba63cea726 *inst/extdata/bams/T1.bam.bai
6e43c101708a4040937e389b9888832b *inst/extdata/bams/T2.bam
b48cfbe384de76d521dff37845bb811b *inst/extdata/bams/T2.bam.bai
1751240dde82ab77847b18cc93ce4b31 *inst/extdata/bams/T3.bam
b0c6a086071d7f7d5c5153cfc1778147 *inst/extdata/bams/T3.bam.bai
0ed841f711101c6ed48133d5cf35c9df *inst/extdata/bams/T4.bam
33e452914d0a92a7287b5902f7a223d3 *inst/extdata/bams/T4.bam.bai
aa1cd7d5f49fc7a5ee7e2721a4654b39 *inst/scripts/createExampleData.R
62e6eb32b9d91e2d2e22f8a0ebe3999b *inst/unitTests/test_analyzeFeatures.R
41062843ebebbec77ddf6fbc1eebe14b *inst/unitTests/test_analyzeVariants.R
1a72ecb53227d3f1a1b3ea90297e911f *inst/unitTests/test_annotate.R
445456f7b917f405ff4ffa9c6f0c305a *inst/unitTests/test_classes.R
fca7f739cb7036e0480477929e575cad *inst/unitTests/test_convertToSGFeatures.R
008fcf1ee84836bd7c707d4e91053124 *inst/unitTests/test_convertToTxFeatures.R
a3b06c1e5dab349b9a3fbacb6ade7563 *inst/unitTests/test_findSGVariants.R
018d012a9bc57431328f9574ad429925 *inst/unitTests/test_getBamInfo.R
49e19e07becae41efb382ed9f01719b2 *inst/unitTests/test_getSGFeatureCounts.R
66d59bb78d566b15751680e3d3fa1c1d *inst/unitTests/test_getSGVariantCounts.R
82ac16fa44fac098647f31ac89dfa696 *inst/unitTests/test_mergeTxFeatures.R
9212fb3c627df1a8f0db8e52fa7b5da2 *inst/unitTests/test_predictTxFeatures.R
e30149b56b868d0e555485ef0607eafb *inst/unitTests/test_predictVariantEffects.R
758795ffc14b7a4b306ed162896fc0fa *man/SGFeatureCounts.Rd
33ef302baaae4c61c895cbf6886a61a0 *man/SGFeatures.Rd
09014a12b279863f0510ba2b879b3c1b *man/SGSegments.Rd
65d664210436de60e8434583ff0a5562 *man/SGVariantCounts.Rd
84ea583e9366119e638887466eb7d16c *man/SGVariants.Rd
061e368533392f779fa7e1a802997f2c *man/TxFeatures.Rd
421298b671a08dbd19670d5b03951f8e *man/analyzeFeatures.Rd
496046be10b15566605c4bf75d390108 *man/analyzeVariants.Rd
6e8d316c635aafd1dad6c96fb8e74eef *man/annotate.Rd
fd4bef79832f0cf5093531796342d232 *man/annotateSGVariants.Rd
62357e15a44cc729aa512021f1b01df5 *man/assays.Rd
538201a37f2866db40773090290d3440 *man/convertToSGFeatures.Rd
4c2eb1535e4fa3ead4897f62151705b3 *man/convertToTxFeatures.Rd
92e9babef6c7a9422cedd6e00173d2d6 *man/exonCompatible.Rd
b702f758041854a195f3f3b7827b8fc6 *man/exportFeatures.Rd
9d2866a40f1b715f01e59190cbbf6c16 *man/filterFeatures.Rd
f080605bdd3098e40356e6c5be5b39e0 *man/findOverlapsRanges.Rd
8fe94cf1257df18f8b9f5b690f675c59 *man/findSGVariants.Rd
00d951c065415e243d176af2f7b7b3e1 *man/getBamInfo.Rd
c7e2065636801263b5de306afb51a79a *man/getSGFeatureCounts.Rd
eb6075b29a80d0309c3454df02b20995 *man/getSGFeatureCountsPerSample.Rd
049bd80513ad7cd4092381c7ca12f6a5 *man/getSGVariantCounts.Rd
aac079f4acdd2773ecf55da3fb572f74 *man/gr.Rd
bd2ad594c5fa6ccf776505318fb9e792 *man/importTranscripts.Rd
36e683456d51cc9e6f490315f3a04555 *man/junctionCompatible.Rd
6452e4ccbbf400ff40906cc3cee27e84 *man/makeSGFeatureCounts.Rd
6555721afa0a77c6f796deeebf9c8310 *man/makeVariantNames.Rd
06400fcaa9e22b6243d8e8e0a284ba6f *man/mergeTxFeatures.Rd
8f6cd7b7d253afa85ae7bb19cb5bb410 *man/plotCoverage.Rd
252b2db65f906d2387e3ca95f9ea7b1d *man/plotFeatures.Rd
6949ce9ae4fd04feb5dfeafd15fa3fdf *man/plotSpliceGraph.Rd
31bf080fdc48b27c6d6e4c9e2a50cfb0 *man/plotVariants.Rd
409a103572ced6eae9d45ec392582083 *man/predictCandidatesInternal.Rd
8ebce2efc2d166742cfb9939242563e0 *man/predictCandidatesTerminal.Rd
83d64b88b5fac78c2c2fe5ccf0acdc10 *man/predictExonsInternal.Rd
a85e3828dd347aefeaaddabf0540008a *man/predictExonsTerminal.Rd
6a2036290505ba2205775a8f4420f43b *man/predictJunctions.Rd
fc47e3ef865b1499662615c9085f3077 *man/predictSpliced.Rd
aae4904407df0fbdd48c39cb5afdc4a7 *man/predictTxFeatures.Rd
7219ef29d1862c67b85ac74a1efd5489 *man/predictTxFeaturesPerSample.Rd
83a98cdee3eeeeed1399fd788e811376 *man/predictTxFeaturesPerStrand.Rd
2871e0d3dcdf029ebaea3bed55806554 *man/predictVariantEffects.Rd
7338bd51b6a10f634b14efed10520e93 *man/processTerminalExons.Rd
3b61a99824b641fe05f8737d661a55a9 *man/removeExonsIsolated.Rd
4359b1ea7d088bc2e625d616bc3b91d2 *man/sgf_ann.Rd
dab897812ff393d6045f717cef11525d *man/sgf_pred.Rd
034f91aa81213b930891ce70fa6307d2 *man/sgfc_ann.Rd
90d00b43a9a47a20dd743493e38fe666 *man/sgfc_pred.Rd
aad7e53eeafca1ed26405e1074b56084 *man/sgv_ann.Rd
c8afa363390e5d02614821c2ba4b0fa4 *man/sgv_pred.Rd
e4e7415a57e8324244bf989dc50acab3 *man/sgvc_ann.Rd
ec10790d6e121c1f645a58c027683097 *man/sgvc_ann_from_bam.Rd
3132fbff1abed00f52f281377a4ab9c8 *man/sgvc_pred.Rd
9b4a23cf4e7cdbc7703a4b32e15695a1 *man/sgvc_pred_from_bam.Rd
792a4c3753c0671c86a3586ff923b156 *man/si.Rd
43ae731a846a2ab42c1c45537e3a2e07 *man/slots.Rd
6020a8b8ba5f1bea3c1cbaee76d5efed *man/splicesiteOverlap.Rd
58bd2e7e02d1426ff79f1a5c6b77783c *man/tx.Rd
9a9e66e3a3e95ed17de3e8ed273cc193 *man/txf_ann.Rd
e1bd38ee25de9d2ed7c4bb5fc496c016 *man/txf_pred.Rd
647de44ff73fcc7c661dfb773c51982f *man/updateObject.Rd
d1a4f9433ee2d38d716fc9680cee2e50 *tests/runTests.R
a1bedcc062dbe7d53c768689aa8c88eb *vignettes/SGSeq.Rmd
db58f370492565967096dab77be6480e *vignettes/SGSeq.bib
f531dd89571d1325edb967e002a8deae *vignettes/classes.pdf
31128171706f5b2d1f2d82f4eb22eb79 *vignettes/classes.png
