c4c136e1ad7668b888ea032149a8dc89 *DESCRIPTION
4cd1cf6a958ca77c604230a2cef6e2a3 *NAMESPACE
13c79f1f810742decda9ed4101198dad *NEWS
0334a9c91c024270384edc489d4f0f8a *R/00.InPAS-package.R
02e46623dbb93d1ccaad6fb1edd6fd1f *R/00.data.R
2aefdaef17c1fad60731efdbfac2cb7b *R/00.get_GCandMappability.R
3a2b1c657d49bf191363b3dc7e0081af *R/00.get_lastCDSUTR3.R
345c71a33b412ca8821e2d10750d6542 *R/00.get_seqLen.R
81cc27c0560c750a3f6e9096ded94329 *R/00.set_globals.R
9d41379add6ca485b47eb17132eae90b *R/00.setup_sqlitedb.R
abe2d978f69f83d726ed752b67b2f7fa *R/00.trim_seqnames.R
479439cfc0dd3d3af7b7c9cbb7a60651 *R/01.parse_TxDb.R
16531fde6d0523864f9d6008bd3e0b09 *R/02.extract_UTR3Anno.R
de3ddc2f900c093c6ffc3d5fbf9d910c *R/03.get_ssRleCov.R
717fdc914c5c40482ad6c0a9c7ab4bcd *R/04.get_chromosomes.R
ade96d85f2671dedc6e0e9f7af5123f8 *R/05.assemble_allCov.R
88275347f58f2caaa626407d83b1b781 *R/06.run_coverageQC.R
ff26fdde8914cd8642188eb884b346a2 *R/07.get_depthWeight.R
f9eef4197bdfa5c313d6b790e3aff261 *R/08.get_totalCov.R
b5264f36f45cfed6b642e028fb647d45 *R/09.get_zScoreCutoff.R
52a01b9b83ce093cdd66b0a40dbef0ea *R/10.get_UTR3TotalCov.R
aaffee6298efd5529a4045a3c0349b46 *R/11.setup_CPsSearch.R
a5a1143b49682e95aa81c4cb0a7b9cd0 *R/12.search_CPs.R
cfaf52c44d91ae7936c352b7f00531d5 *R/13.search_distalCPs.R
1f8d122878bf265c5a29e898fe843134 *R/14.adjust_distalCPs.R
d52b8d864fed160935ce6d4416489394 *R/14.get_PAscore2.R
81166a62c6d32f3debaf359c7540265f *R/14.remove_convergentUTR3s.R
f3634b41a4fd9f8ff1ed9f915a20ed4d *R/15.adjust_proximalCPs.R
807714657b9e673b1f79f28b4d5b1940 *R/15.adjust_proximalCPsByNBC.R
db6399cb64d5d2a4e602159e2a4bc01f *R/15.adjust_proximalCPsByPWM.R
45ebb5938b926ec53bc0d73841eba20f *R/15.calculate_mse.R
a99608af4bfb84c27e6fad534b03eeb7 *R/15.find_valleyBySpline.R
6b78cb3cbc2475a8ced7d5a117626580 *R/15.get_PAscore.R
5355f27682ddd2b2e1877872c60c80f4 *R/15.search_proximalCPs.R
c8b6b37831b19197bfa2470dd62e6b78 *R/16.find_minMSEDistr.R
c55f00ad29d07187b4cce6ab33479345 *R/17.polish_CPs.R
55924f73384aa9286f15be43e8ed3cd0 *R/18.get_UTR3CDS.R
945930acdc492647fb9507e572dfe83b *R/18.get_UTR3region.R
83881737eb20e414a8ecb5dac70ff102 *R/19.get_regionCov.R
c25b4b62a84825845a4c3d5c6d6e2525 *R/20.UTR3eSet-class.R
32f20e5a5088a011672b6da0050245a3 *R/21.get_UTR3eSet.R
da7e9bbac924dd645afc80437b722ce3 *R/22.test_dPDUI.R
3758bfc63a1994245efc4a828e032ea7 *R/23.run_fisherExactTest.R
5d6da6953ce37272dee0fbda1a880b3f *R/23.run_limmaAnalysis.R
3cdf2b216b9f109af4f86f75236fd450 *R/23.run_singleGroupAnalysis.R
7898724cf8f411defe5b659beaddfcf7 *R/23.run_singleSampleAnalysis.R
36b803e5707f334c665302da1b3b4d6b *R/24.filter_testOut.R
04fd7d404339539c42421ba92289ae8e *R/25.setup_GSEA.R
f6cbd08f2c1e6d645381948acaeaf2a2 *R/26.get_usage4plot.R
8823da9c0c3eb92288f89f29dc749e4d *R/27.plot_utr3Usage.R
aaf9d6d03e2f44930cf7b3b4a6c5b49e *README.md
bf05666fdb09d0c949e13188db03e9a4 *build/vignette.rds
4f1e10b36505b87e1e35f3ad99a0e8a0 *data/datalist
fec0efae27f3d375f7a64d3641c2c768 *data/utr3.mm10.rda
b3cb3273763d801825776b14024ea819 *inst/CITATION
071fff853428ccfbd35a82cf4f5c0e15 *inst/doc/InPAS.R
097d36400c083dfdde5df33dae7f65c1 *inst/doc/InPAS.Rmd
ce11cb567f70ed1af329ed51fe780c0a *inst/doc/InPAS.html
fd39ad651f9d1366d13a0d741098d0b3 *inst/extdata/Baf3.extract.bedgraph
fa1e4fe6f1c33d7ca297fa12506a0d2a *inst/extdata/UM15.extract.bedgraph
30f138b6f554fb5e304e86e2d568663f *inst/extdata/eset.MAQC.rda
74350e6c2359aed876a3af9b030509ae *inst/extdata/polyA.rda
6efbed30033c6c24de29bb69dbd583f1 *inst/unitTests/test_get_ssRleCov.R
d00b89fa024cc9604f6fa3fe09d95d17 *inst/unitTests/test_search_CPs.R
a094ad817e49fe6c628129ca7c654ff4 *man/InPAS.Rd
861fd8990021488081748802a7c68943 *man/UTR3eSet-class.Rd
30a5780e788dfbc4292251db7bf71314 *man/addChr2Exclude.Rd
f1e92c97e1bdeccb70986d6ddb1f7b5e *man/addInPASEnsDb.Rd
04bcfabbb611c07c843864d8c567c74c *man/addInPASGenome.Rd
36b79632f5da986a5ca85917cee3ea1b *man/addInPASOutputDirectory.Rd
60d9bb7e4389b4ef2b374a807176e7ac *man/addInPASTxDb.Rd
ac3dc5c891c3ea09119e70d96ae634f7 *man/addLockName.Rd
6119d1abd8ec178b83bb8ba96ccba3d7 *man/adjust_distalCPs.Rd
783fe2d0eab5c8f78463cedc2bd050d0 *man/adjust_proximalCPs.Rd
375eac1640ecfa0d8183856b36ca8b0b *man/adjust_proximalCPsByNBC.Rd
f1059890f50da23966524fb3953e6d95 *man/adjust_proximalCPsByPWM.Rd
657c74928e3b44c6b2a9b0455a607a47 *man/assemble_allCov.Rd
11554d1217f30b3af5381f31ae30530f *man/assign_feature.Rd
2cb1114844882f1ba0cb4d2682be08f0 *man/calculate_mse.Rd
8bf64e91c7f7cd844cd31d655cae6760 *man/compensation.Rd
a1d94bb24376bf5f29ad29dc2bd78fc4 *man/dot-onAttach.Rd
a9d3ab67acb936dac55a283dad479ff4 *man/extract_UTR3Anno.Rd
5fcdde573a0c104ad624bd875705f8ee *man/fft.smooth.Rd
988321cb348022a06e8693b94da7ffd8 *man/filter_testOut.Rd
604afe990697b320aa019d77ea2ca2f8 *man/find_minMSEDistr.Rd
ac1622af12299feec8041f6c382a97ad *man/find_valleyBySpline.Rd
b8c763f21f13d3e7c8b640d4bb89b016 *man/gcComp.Rd
f306ac93a3911cf5e48a6ebe7fc077ca *man/gcContents.Rd
c81c827c0bc69ac1fa41d6fb2ba54ff8 *man/getChr2Exclude.Rd
249f65602fc96770a3a44ee4a83af9e3 *man/getInPASEnsDb.Rd
1563983702454dd8558e04fa56451de4 *man/getInPASGenome.Rd
358ff31671847fce1da3cfd1c5b2617a *man/getInPASOutputDirectory.Rd
973d89ca9d9b2ee9f4bd903edd95414a *man/getInPASSQLiteDb.Rd
ae67375e9bec4ec6297f5bf1db671fd8 *man/getInPASTxDb.Rd
74df6c2fc743d332399106805e0ca173 *man/getLockName.Rd
8235925c40733a55fd0b1d8978ac6e9e *man/get_PAscore.Rd
f440090e6c87c02f1dafd31385e7c7e7 *man/get_PAscore2.Rd
d142f7407eb42e8d403cdea64a2f5669 *man/get_UTR3CDS.Rd
f34d166a04114879ea4014e4ae9ca06c *man/get_UTR3TotalCov.Rd
6dbdf582444573ab23d643a4fcdfc53f *man/get_UTR3eSet.Rd
ee0204dfab4d644fda6e403f1ee5317f *man/get_UTR3region.Rd
c67a0d7c7f00af4e9f460bd54573efc1 *man/get_chromosomes.Rd
9e4639e23f05e098b675921fedd137c9 *man/get_depthWeight.Rd
cf43c4d1386c56421a981d792ca0deb7 *man/get_lastCDSUTR3.Rd
96e1767332b8b1eeea22bfa156e570a5 *man/get_regionCov.Rd
85abb6c72e8274f5c91dd6f150046ee1 *man/get_seqLen.Rd
6864b8ce20fe67f94b610db6258e531e *man/get_ssRleCov.Rd
5565be15f9c0cda1b989dedb0bbd05f7 *man/get_totalCov.Rd
1eae2a19e89c7497e407b26c14c7f344 *man/get_usage4plot.Rd
77798f3956b063d658ec3d7790a0a3b2 *man/get_zScoreCutoff.Rd
1b79ca02c9d713a100e9d4d49c0f581a *man/mapComp.Rd
bd577ed5c801d3036552dfffe6316b8c *man/parse_TxDb.Rd
e8a8f344c1b8010796ec60ae2fe7a22b *man/plot_utr3Usage.Rd
1149c28b7ea1698f211ae81a06a5c4b3 *man/polish_CPs.Rd
1fc4edfbab9633fa5d7bc7b239fd6cad *man/remove_convergentUTR3s.Rd
28a3abd5263070e75a91a44b28e9c364 *man/run_coverageQC.Rd
9c33e9f5e4c60a0db9a478edd54afee8 *man/run_fisherExactTest.Rd
6528a5ee1072c4e0eca84811cf7f5fe2 *man/run_limmaAnalysis.Rd
98b9e716d9292a1a89047f62222caa07 *man/run_singleGroupAnalysis.Rd
a59a4c4f68f4cdd1cd67a51ef7d4d7cc *man/run_singleSampleAnalysis.Rd
5ca56a951c91963010fdd3c219c14b1d *man/search_CPs.Rd
e5d27b32025bb9f7d4334c8d2cb9dd6d *man/search_distalCPs.Rd
880b24f9944dc0d211c934b4c818d07c *man/search_proximalCPs.Rd
35e18999f2e4fa69bc6aa19a9d1d907e *man/set_globals.Rd
4f1cac494bc6980e13f9d2822a72499a *man/setup_CPsSearch.Rd
b7b35a6485c3100e61aa17b40a2b7973 *man/setup_GSEA.Rd
2ef24080d456fb227fc9823aa398df28 *man/setup_parCPsSearch.Rd
0fef408bd3d4bbf14dd14bd8fa339575 *man/setup_sqlitedb.Rd
df8fbf66e726774238f2834717ddd06e *man/test_dPDUI.Rd
705c62b6cd53cf8034f771dd51ee9d85 *man/trim_seqnames.Rd
15ef7af024c316579a14ecdd93539982 *man/utr3.mm10.Rd
d92af863da4c23b6c315cfe42bc20289 *tests/runTests.R
097d36400c083dfdde5df33dae7f65c1 *vignettes/InPAS.Rmd
2fcaf97a783a254afac21cc1d2e44b8c *vignettes/nature.csl
8ae82cd3750b372db47a665f43319545 *vignettes/ref.bib
