1d9670df9065b874c905c574f4776a09 *DESCRIPTION
d53cf4ec47fb6033dc7a204bd8599be1 *NAMESPACE
7872663b974430f59a2ebc0ceee04e99 *R/breakTranscriptsOnGenes.R
aeb466d408eb05f5603a447eae0ca77e *R/detectTranscripts.R
b4bb44922d0a709bc1a0ce2b2ce75c6b *R/expressedGenes.R
3f56c36522f440d0f70c67a7b288199b *R/fitDistributions.R
d3b313ad0d8d7289f301f43865abbe0c *R/getTxDensity.R
378c481aa6603e9be99d85c9457ef226 *R/limitToXkb.R
31044cff26da114f5bb4c08e1e3affd9 *R/makeConsensusAnnotations.R
a1224dd49dcb31701bc3eb2a3ce65a5c *R/metaGene.R
9f9fe14639896756991582ce3edf3dc1 *R/pausingIndex.R
b5a05239938ff5bc2217974b7556b384 *R/polymeraseWave.R
bf69e3356bf15e73e91c145c95203061 *R/tlsFits.R
05b58afe1103940ce83029ec20fac685 *R/windowAnalysis.R
a258cb341ab46121491f443514abf01b *R/writeWiggle.R
72059f9212be8539b3ab2849b4f570ee *R/zzz.R
079d0f40019725d430f4ae1c1db516fb *build/vignette.rds
6841c3e407b7cecdf26485fe2877c564 *inst/CITATION
2006d41fb8c790a5a260d649dd6b6d0c *inst/NEWS
85e2ee359983c5f3697ee8516e9b1a41 *inst/doc/groHMM.R
6405b413cb9f04f7759bcaa555b8b20c *inst/doc/groHMM.Rnw
2138be8d50c23acce415df394de0915e *inst/doc/groHMM.pdf
1841d24ed32b10fb1c822130573a9dda *inst/extdata/S0mR1.bam
3d2b9726ac40180c6d991ddecbaf53ac *inst/extdata/S40mR1.bam
e2a57607a39751e6f29f97bc5aba9d51 *inst/extdata/Vignette.RData
892d23ccd0c31913e1897a0f12178c5f *man/RgammaMLE.Rd
e1d0fc79eb4d2d53a7edbd9b1ef296e2 *man/Rnorm.Rd
8e36a750337603aad2899daa4037b070 *man/Rnorm.exp.Rd
eef05bf091890a981d1ecf9030bf1d09 *man/averagePlot.Rd
fa09a30e10f362efd704f2443f94dc8d *man/breakTranscriptsOnGenes.Rd
4c4b73b60aacf88abab40dd6269c1f44 *man/combineTranscripts.Rd
92045f7ac0dfc476dc11f1d19f28703e *man/countMappableReadsInInterval.Rd
db1a5b08109d4d07804131b5ff242d3f *man/detectTranscripts.Rd
427a9c5b9316d5c41997211ceafc037e *man/evaluateHMMInAnnotations.Rd
cf4f557e6783833c55fd2fe302433b65 *man/expressedGenes.Rd
0c9345f8bf4e99bedbaa10de450935aa *man/getCores.Rd
c85a4f5a1f3eb3a2579b963eb869bf67 *man/getTxDensity.Rd
0f27cab7916acd9802ec54903f57367f *man/groHMM-package.Rd
6816ee8ac6f21c2d8297131ca40af04f *man/limitToXkb.Rd
089d5c2434232417a294a2264858471b *man/makeConsensusAnnotations.Rd
3b3bda6ce39324c1ed8c2e2e7bc2e89b *man/metaGene.Rd
8aa644a7bb38a84b1a818984b6684b95 *man/metaGeneMatrix.Rd
4d37f69f8bd7bfb1d0b77330d7da4754 *man/metaGene_nL.Rd
aa8119a56a32b37e46b699d11ca1e7d6 *man/pausingIndex.Rd
1b1b92f8085068d326a1b8974cc8b99d *man/polymeraseWave.Rd
ac9c226bbaa84195b6e5741f7446eed5 *man/readBed.Rd
92a0ea8008661662ede520ec625e41c5 *man/runMetaGene.Rd
c75f87db2833a9138ce98e40d4826aaa *man/tlsDeming.Rd
a74f12f05bc8e4a5e7b16417bf47193d *man/tlsLoess.Rd
a5aedf6856f0fbd3d2b3c04047b81b59 *man/tlsSvd.Rd
502631ec180c2658386a6a8b085a7085 *man/windowAnalysis.Rd
2413e530bb54c8c5af5512f3e1fcaf17 *man/writeWiggle.Rd
3d1a13b322c4296fab6199ff3724861d *src/AnnotateProbes.c
9c53488a70372937303387e4fb8c72a5 *src/DecayAlgorithm.c
f612a77f46b6efa5fb79287e61da1c92 *src/MLEfit.c
45e475e8012b269402ee192fadb5ff52 *src/RegisterRRoutines.c
2a48ad3c0cb2f467cdad922baa402952 *src/UsefulValues.h
f206d36c716c5b92a1bedbeb698a2821 *src/Windowing.c
8c41f5520fb2b919d86c0c1fcd9675b3 *src/hmmEM.c
73833840f471e044248ca3c0fc5209ef *src/hmmFwBw.c
d968e85616d46e1aa820532c36c66485 *src/hmmHeader.h
8f3fab594e03238749cbae6ed9a87941 *src/hmmMiscFunctions.c
7ea293a3971e23f008f3960f4fbd1bbe *src/hmmViterbi.c
98d7117157b1b64d22011fdee32a49ad *vignettes/GROseqData.png
08eca12a59925c786d7585df788cb751 *vignettes/GROseqHMM.png
6405b413cb9f04f7759bcaa555b8b20c *vignettes/groHMM.Rnw
1220f68e424714c4af7f21a5f5d205a4 *vignettes/groHMM.bib
