5471032b96cd4ae7d11c705e0e94b2fa *DESCRIPTION
720167ce2456768652ed7e56aa5e04f2 *NAMESPACE
d182f414729dd77692fc334276542d06 *R/breakTranscriptsOnGenes.R
ba7cc91d48d426c4a5d1dac4b13fb04a *R/detectTranscripts.R
6063f791cfe7563f4f42e5a4a3343780 *R/expressedGenes.R
a15562a68306cba6ccd8f8aa027b2027 *R/fitDistributions.R
ae05f90edfda8ce1776faa6995948c90 *R/getTxDensity.R
99f68d34f4c06d023a738bb668fc876c *R/limitToXkb.R
921621a0b820603a5d23d6ed6b0b2c0e *R/makeConsensusAnnotations.R
cf7a8a0e1a806ab91d41282b34406236 *R/metaGene.R
e97df6a10d017c9fe6fb113e0f9f1797 *R/pausingIndex.R
af7face9d23bb5133c6a3d9f7007a9fd *R/polymeraseWave.R
2398db9accacf3ec77ce4d8e2dbfe406 *R/tlsFits.R
960f66562a5e81d68f18e8630f20a1aa *R/windowAnalysis.R
f72657ad6e3bffbb0ace8002eda04ba3 *R/writeWiggle.R
72059f9212be8539b3ab2849b4f570ee *R/zzz.R
febce9986c0704a99cbf3aebf2343ff9 *build/vignette.rds
6841c3e407b7cecdf26485fe2877c564 *inst/CITATION
2006d41fb8c790a5a260d649dd6b6d0c *inst/NEWS
587f8d473834ffdc13ea7a062a4b8ac3 *inst/doc/groHMM.R
46d2fae674d566841c9b8e392ef955d7 *inst/doc/groHMM.Rnw
0e7f0b8944c6ae0132b595f98b9591cf *inst/doc/groHMM.pdf
1841d24ed32b10fb1c822130573a9dda *inst/extdata/S0mR1.bam
3d2b9726ac40180c6d991ddecbaf53ac *inst/extdata/S40mR1.bam
e2a57607a39751e6f29f97bc5aba9d51 *inst/extdata/Vignette.RData
d89b2dc7e848db3237c3b5cf99d3afd6 *man/RgammaMLE.Rd
2402f533b0c5dea57b74d5d9dc19745d *man/Rnorm.Rd
e55230ca78d4ddebfbe69f9696a5861a *man/Rnorm.exp.Rd
b9541c2119cd47cca05c5ed9edd25921 *man/averagePlot.Rd
77369b818e8d5d50702eacbb9e18b484 *man/breakTranscriptsOnGenes.Rd
0a31773fe03975f9e96e6db5b7431758 *man/combineTranscripts.Rd
c988f18c4a60605d91ed0072014a7add *man/countMappableReadsInInterval.Rd
668ff049fcb44cba9a0ac4cf9ef3adee *man/detectTranscripts.Rd
ff715d6ec9e5827f92218f1392bfa785 *man/evaluateHMMInAnnotations.Rd
94cbe7f8b0565e0ff66def2822fe955b *man/expressedGenes.Rd
39b15516e90d1519b537de54c856d96a *man/getCores.Rd
f2524450525fbce3e630102b0be8ccb5 *man/getTxDensity.Rd
0f27cab7916acd9802ec54903f57367f *man/groHMM-package.Rd
8dd2b597528bb665fba29cadce367bce *man/limitToXkb.Rd
5746685d0333e5f50ff06625579b773a *man/makeConsensusAnnotations.Rd
017647e41cd53e9caf3d0fdd9a06612f *man/metaGene.Rd
7a4512f819dd341ef8470e53e25780af *man/metaGeneMatrix.Rd
e92c891bbd3f6071b1ebbb9579964c48 *man/metaGene_nL.Rd
42ebcac695475bb7d65e7de4b958d8a5 *man/pausingIndex.Rd
1ed3bd5b5887ed4a010a031e2a2b8078 *man/polymeraseWave.Rd
0ae98d20bd7d9b0788d4f1da4df48dc6 *man/readBed.Rd
f3acb94028692f1749141b7bc5413324 *man/runMetaGene.Rd
3df9ba4a4b542b17fda87957abd2566b *man/tlsDeming.Rd
eaf194ebbc7e5d98881fc560a7550446 *man/tlsLoess.Rd
6332e56124d90edc3204ac557f0fbfc9 *man/tlsSvd.Rd
fdd33ac5b47c42ec02d7a9351ab9593b *man/windowAnalysis.Rd
e4824a2e9ea83c4b81b5bed0a6f28c8e *man/writeWiggle.Rd
3d1a13b322c4296fab6199ff3724861d *src/AnnotateProbes.c
77187a4daba6f2b3f21973965ad99a25 *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
fa566f79bff0e8a86fc9e7001fa7e405 *src/hmmMiscFunctions.c
7ea293a3971e23f008f3960f4fbd1bbe *src/hmmViterbi.c
98d7117157b1b64d22011fdee32a49ad *vignettes/GROseqData.png
08eca12a59925c786d7585df788cb751 *vignettes/GROseqHMM.png
46d2fae674d566841c9b8e392ef955d7 *vignettes/groHMM.Rnw
1220f68e424714c4af7f21a5f5d205a4 *vignettes/groHMM.bib
