ef25ac6d2e5af65d672899ea69282314 *DESCRIPTION
dcc1616728d4807ab078554210f6c83f *NAMESPACE
4d194d38b0565645e217206b29cf34dc *NEWS
0334a9c91c024270384edc489d4f0f8a *R/00.InPAS-package.R
02e46623dbb93d1ccaad6fb1edd6fd1f *R/00.data.R
41137d340bda5bca46be1634160293d8 *R/00.get_GCandMappability.R
71db356b553ce740dc7fe9d33de882a6 *R/00.get_lastCDSUTR3.R
9150cc51dcaec682f7e8bf6d28586d1d *R/00.get_seqLen.R
42d941dcd665bfcee6832e22301c6e4c *R/00.set_globals.R
9d41379add6ca485b47eb17132eae90b *R/00.setup_sqlitedb.R
abe2d978f69f83d726ed752b67b2f7fa *R/00.trim_seqnames.R
0f087b624913225e03a23a470bbf02fe *R/01.parse_TxDb.R
c7c7523fae58faab01927c93596e7ec0 *R/02.extract_UTR3Anno.R
1e00d20a8e32dc37022f6b344ea7164c *R/03.get_ssRleCov.R
717fdc914c5c40482ad6c0a9c7ab4bcd *R/04.get_chromosomes.R
ade96d85f2671dedc6e0e9f7af5123f8 *R/05.assemble_allCov.R
522e9888b6568e1ad21c64b09658994f *R/06.run_coverageQC.R
ff26fdde8914cd8642188eb884b346a2 *R/07.get_depthWeight.R
f9eef4197bdfa5c313d6b790e3aff261 *R/08.get_totalCov.R
b5264f36f45cfed6b642e028fb647d45 *R/09.get_zScoreCutoff.R
19fcf41023e54feb63d6de5f562dc08a *R/10.get_UTR3TotalCov.R
3fff8ff52892b1474e4b8d682ff968ff *R/11.setup_CPsSearch.R
bc40029a048d08a41319b2435d529c20 *R/12.search_CPs.R
0e6e88da278d222de932083262d962f6 *R/13.search_distalCPs.R
1d8defe7706ef317287689341fa53171 *R/14.adjust_distalCPs.R
d52b8d864fed160935ce6d4416489394 *R/14.get_PAscore2.R
f1a27876c657ff29d60941301e95b078 *R/14.remove_convergentUTR3s.R
af48ab93fc2b9ac69bb3e6f30f4a3db4 *R/15.adjust_proximalCPs.R
508d490e74b98a6c4ad64544c88a950c *R/15.adjust_proximalCPsByNBC.R
0347420cec469586e12e03ce0ca2a472 *R/15.adjust_proximalCPsByPWM.R
45ebb5938b926ec53bc0d73841eba20f *R/15.calculate_mse.R
a99608af4bfb84c27e6fad534b03eeb7 *R/15.find_valleyBySpline.R
6b78cb3cbc2475a8ced7d5a117626580 *R/15.get_PAscore.R
8b07d375e56fd5bd8866208da04098aa *R/15.search_proximalCPs.R
c8b6b37831b19197bfa2470dd62e6b78 *R/16.find_minMSEDistr.R
c55f00ad29d07187b4cce6ab33479345 *R/17.polish_CPs.R
49af5236a7e8927b66dba4d2083b2be7 *R/18.get_UTR3CDS.R
945930acdc492647fb9507e572dfe83b *R/18.get_UTR3region.R
83881737eb20e414a8ecb5dac70ff102 *R/19.get_regionCov.R
bd52e70dee15a26b7f93338f4f4de73c *R/20.UTR3eSet-class.R
e26f14536da6f0aeb53faf10dc4cf463 *R/21.get_UTR3eSet.R
da7e9bbac924dd645afc80437b722ce3 *R/22.test_dPDUI.R
3758bfc63a1994245efc4a828e032ea7 *R/23.run_fisherExactTest.R
5d6da6953ce37272dee0fbda1a880b3f *R/23.run_limmaAnalysis.R
d1a9e6a8ec4717994c121b686edcbeac *R/23.run_singleGroupAnalysis.R
64d9690535f43f1d282af58d59a17db6 *R/23.run_singleSampleAnalysis.R
36b803e5707f334c665302da1b3b4d6b *R/24.filter_testOut.R
04fd7d404339539c42421ba92289ae8e *R/25.setup_GSEA.R
f6cbd08f2c1e6d645381948acaeaf2a2 *R/26.get_usage4plot.R
01c97181d564c614dd32b0f877050417 *R/27.plot_utr3Usage.R
aaf9d6d03e2f44930cf7b3b4a6c5b49e *README.md
f71444d36ecfe6852b2ac165dbf5ed9f *build/vignette.rds
4f1e10b36505b87e1e35f3ad99a0e8a0 *data/datalist
fec0efae27f3d375f7a64d3641c2c768 *data/utr3.mm10.rda
b3cb3273763d801825776b14024ea819 *inst/CITATION
071fff853428ccfbd35a82cf4f5c0e15 *inst/doc/InPAS.R
097d36400c083dfdde5df33dae7f65c1 *inst/doc/InPAS.Rmd
c711debf9bbcffb7ad66c96a06d28954 *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
d6fa3c282453249eedb6c69bb5061f59 *man/InPAS.Rd
a7705faf3b19c9c4cb374ea9460510cc *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
8366a1e56a2bc2fad0ee1453b9638e15 *man/extract_UTR3Anno.Rd
5fcdde573a0c104ad624bd875705f8ee *man/fft.smooth.Rd
57759c8c23c8cf90a2bffc527950e1be *man/filter_testOut.Rd
604afe990697b320aa019d77ea2ca2f8 *man/find_minMSEDistr.Rd
ac1622af12299feec8041f6c382a97ad *man/find_valleyBySpline.Rd
7698859283f596a44dafaea4e0cf5878 *man/gcComp.Rd
712c64e04df069296540d60688497780 *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
3ba03a70e61ee5700f1c2bd3c8ec696d *man/get_UTR3TotalCov.Rd
0b97a27ecbd9247f3f43056b872c8776 *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
4875cadc7ceff4a058d2b31374a0613d *man/get_seqLen.Rd
8240494244c11fa9422939adade728c5 *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
6d3f052980339f299e8a39c0b9fb6c93 *man/plot_utr3Usage.Rd
1149c28b7ea1698f211ae81a06a5c4b3 *man/polish_CPs.Rd
1fc4edfbab9633fa5d7bc7b239fd6cad *man/remove_convergentUTR3s.Rd
28a3abd5263070e75a91a44b28e9c364 *man/run_coverageQC.Rd
8e98984888b13c54b61b3de5788b4919 *man/run_fisherExactTest.Rd
d5b14c2668209bed0eaa2912999b34c1 *man/run_limmaAnalysis.Rd
5c07ca987129b78dbdf2a93bae4a8f49 *man/run_singleGroupAnalysis.Rd
3ca949d4a322f9ac392ba8f3d98296af *man/run_singleSampleAnalysis.Rd
22564b8261799adb92a54b719d1138c2 *man/search_CPs.Rd
e5d27b32025bb9f7d4334c8d2cb9dd6d *man/search_distalCPs.Rd
880b24f9944dc0d211c934b4c818d07c *man/search_proximalCPs.Rd
baaf116d8b4951904e6b0bc8b536f5a7 *man/set_globals.Rd
4f1cac494bc6980e13f9d2822a72499a *man/setup_CPsSearch.Rd
76382df3472d30af052eccacb1f6d84c *man/setup_GSEA.Rd
2ef24080d456fb227fc9823aa398df28 *man/setup_parCPsSearch.Rd
0fef408bd3d4bbf14dd14bd8fa339575 *man/setup_sqlitedb.Rd
96a44fc50a25e46b259420801beff818 *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
