e506bc08d211da8380bd6175f6caa837 *DESCRIPTION
192d4abf909b6935229b2e188423d537 *NAMESPACE
4ef60fce70e17092c70e9ff7bd693bdd *NEWS.md
87164eb22c9ca60d8a8b6061e8467ff2 *R/TrIdent-package.R
0af10ad5af68f8f50450423a2717615e *R/TrIdentClassifier.R
363ea9b4bebff3e031ba9beea5ddef9f *R/TrIdentSampleOutput.R
9d5a8af6d78e521b272398f56faed5b7 *R/UtilFunctions.R
9bae316367c23910a2c52de4936f7e9e *R/VLPFractionSamplePileup.R
f232a9c39d653c8bb2c84815180e77f6 *R/WholeCommunitySamplePileup.R
d1ca2dbe2b7477190bd96102525fef2d *R/blockPatternFunctions.R
66f2439070fd6ee37bf5f7332127e9ed *R/fullSlopingPatternFunctions.R
5f3545090486d2c0faaf4fabaad7307b *R/noPattern.R
0a6ee588f7f7ed5965bd0c0670f9a5f9 *R/partialSlopingPatternFunctions.R
337ecf57f8764904416b70355c269b1b *R/patternCharacterizationFunctions.R
33d2190895a6d45efd8677e64e7a5ad5 *R/patternMatcher.R
991631cd15308debe0b68449e00a0645 *R/plottingTrIdentResultsFunctions.R
a4997e45bb29660e276ff35220fb1a68 *R/resultsHisto.R
753d25507191245ef10d1484505faf51 *R/specializedTransductionHelperFunctions.R
c6087849fc1b6711dfbfaf43715a5440 *R/specializedTransductionID.R
4b137cde33d7ec00f4c265fcc03ebfe2 *R/summarizeResultsFunctions.R
fd810f466a1470438fd74d243c3ad4f9 *R/sysdata.rda
10f937e8200cc6c6297a5b09dc9ba637 *README.md
f9baea62f243071ff2b8aef0600dfae3 *build/vignette.rds
806f707c5d23a2f4c5fda35d2684869e *data/TrIdentSampleOutput.rda
31982e6044a37c19e1078f414f12732b *data/VLPFractionSamplePileup.rda
b1089bb188c3f28cf9e9b6a6eeb1737a *data/WholeCommunitySamplePileup.rda
03faf8f52cdb9be96f1b367ac439584f *inst/doc/TrIdent-vignette.R
8515608eab49ea4bd2bc72a4491c38da *inst/doc/TrIdent-vignette.Rmd
61c18e60f265b7d7e7f847be25fb362b *inst/doc/TrIdent-vignette.html
b70fd1b0e6488cb414577ebb80f80499 *inst/script/GenerateSamplePileupFiles.txt
142481c5955690052dc2eef992b1116f *man/NARemover.Rd
ae9e82bd0fa299cee78d25316bacdbbf *man/TrIdent-package.Rd
716a01fc3750c25018ff159637819bdf *man/TrIdentClassifier.Rd
930e18279d8de2551ea9cb854a57e380 *man/TrIdentSampleOutput.Rd
28dcf39ea346fdda2de72ec849c212c8 *man/VLPFractionSamplePileup.Rd
f15036c906af9aec5263494964030f68 *man/VLPtoWCRatioCalc.Rd
49a85f61445c7fc09cb7a04025cbe38b *man/WholeCommunitySamplePileup.Rd
2c85e3b169903b32411a02a550c2fdd0 *man/allPatternMatches.Rd
b55156bb34aa10399378a6bdfc9f7d82 *man/allProphageLikeClassifs.Rd
693abb1096018a358682d800087f310a *man/allSlopingClassifs.Rd
21df65cb495ece852b31c5ab53956e3c *man/blockBuilder.Rd
738b9ff4236527992e16d6be38ffb2bf *man/blockTranslator.Rd
eb408a0ce217f291a0fd8e02ac1b1ada *man/changeSlope.Rd
62fb5badd83c6028a8d57546e8488a3a *man/changeSlopeWStart.Rd
f85ad3665d62297d43ed27af2ff114cd *man/changeWindowSize.Rd
df9161e5fd2aafe01c26377337f579bf *man/contigClassSumm.Rd
c1ffa24fb27de38bbdaaf06b2b0305a8 *man/directBlockBuilder.Rd
689055224827c1cf9908ec0c9d714081 *man/figures/README-example-1.png
bf129bc829e77c7fd5667d998476a2c0 *man/figures/README-example-10.png
bf0b1b3ad5bfae4277b794379918b03d *man/figures/README-example-11.png
d76767d4c9c116ff9aafabac4ce0f5d2 *man/figures/README-example-12.png
d76767d4c9c116ff9aafabac4ce0f5d2 *man/figures/README-example-13.png
101a2869619da6db4090fd3bfad37252 *man/figures/README-example-2.png
611134cc339507aefb87b3e71e46896a *man/figures/README-example-3.png
2a80f3b6a65f4dec9689fe9e3078b463 *man/figures/README-example-4.png
65ffbd9507f668d45231c868eca0baab *man/figures/README-example-5.png
c9665a4f8648dab9622cf19fd703c23d *man/figures/README-example-6.png
e61bed567879b961fda90fd7b266d618 *man/figures/README-example-7.png
5b01c0c6f30c799db2c7ee5184af7076 *man/figures/README-example-8.png
d6a6aee78042700d1a9f6ea23ae2a57c *man/figures/README-example-9.png
3aa239f5ba7ddee8a8f403f216c5a0a6 *man/figures/logo.png
66b0c9f79e89a954c644a962747cda9c *man/fullSlope.Rd
fac4d434b2967fa80f4128b3e2e3044f *man/leftRightBlockTranslater.Rd
79b48a40fa42fb41619cf95eefec2126 *man/makeBlockPattern.Rd
3e83eccbb43d0034f13cc54a538cb31f *man/makeFullSlopes.Rd
706782219a8e9a98ee8eebe1f797ade9 *man/makeFullSlopesDirect.Rd
745d32a26b18047590d7fb6dfe913d51 *man/makeSlopesWStarts.Rd
52129d86ee992514e84fd81847bdfd60 *man/noPattern.Rd
97dc7080b43b2dd3b96c79e6b78b22b8 *man/optimNoPattern.Rd
ba41a548334554c41ca9b37054ed054c *man/optimSlopeFull.Rd
b310d0f5cf45ccf1a1c10c30d23d48f0 *man/optimSlopeWithStart.Rd
daed69ec8a3da05178109dcf400a59e7 *man/patternBuilder.Rd
69d6c09bc8aef288443317b3776a690a *man/patternMatchSize.Rd
b0b3472e19746d66277fc17effe10b93 *man/patternMatcher.Rd
d063c9127e887758bfb34ea912275361 *man/pileupFormatter.Rd
030a7a34aaadff615f38816f40114cd6 *man/plotTrIdentResults.Rd
e0d5ee4b755ac368a17641ac609e22af *man/prophageLikeBorders.Rd
e68b4d2444ab0592f821b756fb042164 *man/prophageLikeElevation.Rd
637a952437a27f9d99bc1f9aeeb97a6c *man/prophageLikeZoom.Rd
304ceacf7e0181d74e4967df2e23faab *man/resultsHisto.Rd
8183c3a3bddcdf6d97ed3ca4c6e2b501 *man/slopeSumm.Rd
08dfdac73964b2dd29e719737b2a4e86 *man/slopeTranslator.Rd
00fd41c4cc8748c24b9d941f9230d0a3 *man/slopeWithStart.Rd
c8b5b9916cc98f21c1ab95cdfe2299db *man/slopeWithStartDirect.Rd
72b26b953443bbb5fa13e369fc37efff *man/specTransductionPlot.Rd
4b1fccee7592389eb5fe747d774529b6 *man/specTransductionSearch.Rd
41888206ad27e624637e0c3ab2e4ea3a *man/specializedTransductionID.Rd
7907a3ef440638d71c1ba3c06b6f634e *man/zeroCountSearch.Rd
8515608eab49ea4bd2bc72a4491c38da *vignettes/TrIdent-vignette.Rmd
