203dc672fece98a92f26496836c5f30d *DESCRIPTION
eaa6e10d0d6fea69e2f90baa41790150 *NAMESPACE
111ff9fb50fc7cd19c87c376aa22099a *NEWS.md
87164eb22c9ca60d8a8b6061e8467ff2 *R/TrIdent-package.R
ff247426025cdf8a5ad0c39c8cf1580b *R/TrIdentClassifier.R
363ea9b4bebff3e031ba9beea5ddef9f *R/TrIdentSampleOutput.R
9d5a8af6d78e521b272398f56faed5b7 *R/UtilFunctions.R
9bae316367c23910a2c52de4936f7e9e *R/VLPFractionSamplePileup.R
f232a9c39d653c8bb2c84815180e77f6 *R/WholeCommunitySamplePileup.R
82b90dadfe48bf4364708d59d71b3819 *R/blockPatternFunctions.R
34610e5ff7e1760b1e00827c9a0b7ee1 *R/fullSlopingPatternFunctions.R
9b4b88a73a442ff5c42a66f9510b4f19 *R/geneAnnotationSearch.R
ece8437998c25086902a2dd338e143f2 *R/gffSample.R
33d8357627e8fefd520a03b226dd64d1 *R/noPattern.R
62d9be67847e2223c0d973b23787d41d *R/partialSlopingPatternFunctions.R
337ecf57f8764904416b70355c269b1b *R/patternCharacterizationFunctions.R
10f8ef833e0619d8255aad894bde25bf *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
b567886f6f4e234f4804adcbc14eb159 *README.md
e48119d71660f3a352237496600c4ab3 *build/vignette.rds
806f707c5d23a2f4c5fda35d2684869e *data/TrIdentSampleOutput.rda
31982e6044a37c19e1078f414f12732b *data/VLPFractionSamplePileup.rda
b1089bb188c3f28cf9e9b6a6eeb1737a *data/WholeCommunitySamplePileup.rda
7907200f5f2e9da32aaaecb332cdc42b *data/gffSample.rda
47923e49b9117991c4a9a8a3383ef02b *inst/doc/TrIdent-vignette.R
7a44d7d9a30b1442cbcd227b6fe1ed77 *inst/doc/TrIdent-vignette.Rmd
4af3d1827b271a0938104f457df837d6 *inst/doc/TrIdent-vignette.html
b70fd1b0e6488cb414577ebb80f80499 *inst/script/GenerateSamplePileupFiles.txt
142481c5955690052dc2eef992b1116f *man/NARemover.Rd
ae9e82bd0fa299cee78d25316bacdbbf *man/TrIdent-package.Rd
adff47305dd2b98346d3462ff3beced8 *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
d2e64004cddaa3dd95c4c4a6e394553c *man/blockBuilder.Rd
738b9ff4236527992e16d6be38ffb2bf *man/blockTranslator.Rd
eb408a0ce217f291a0fd8e02ac1b1ada *man/changeSlope.Rd
62fb5badd83c6028a8d57546e8488a3a *man/changeSlopeWStart.Rd
f85ad3665d62297d43ed27af2ff114cd *man/changeWindowSize.Rd
df9161e5fd2aafe01c26377337f579bf *man/contigClassSumm.Rd
d6e4541e765fdb7d693057df59c74109 *man/directBlockBuilder.Rd
615269098bd1d725605fbf9c5dbd49eb *man/figures/README-example-1.png
ad6fdc488c211d98827a31a512771bb1 *man/figures/README-example-10.png
a0475556b4304a807ff290ef0e1f2ada *man/figures/README-example-11.png
4d7f9aa81638d5c887a8e621da10f6d7 *man/figures/README-example-12.png
8cc3cca7499cbca77e4f13766c31ed3f *man/figures/README-example-13.png
7a8f67d795e072b0eebc9a01254b4919 *man/figures/README-example-14.png
4188f5347b0380a18e24d3a9b7904048 *man/figures/README-example-15.png
92de89cb10068b07765a27599f896cb5 *man/figures/README-example-16.png
06c622a9df269413c82473984dfd268d *man/figures/README-example-17.png
f81320d04a2edc2cebb017d5244d96a1 *man/figures/README-example-18.png
69c6e2c26480b4f1f444a16ab858d832 *man/figures/README-example-19.png
73ec834bd7ff04ae1cd1487d0cbe9a3f *man/figures/README-example-2.png
d6b5661fd1d91b4d7bb1cfd0476d15f8 *man/figures/README-example-3.png
0a7ce244c723b2605d202db6f469a4ae *man/figures/README-example-4.png
b4fa1d00fcefacd42cd418f25fe3a417 *man/figures/README-example-5.png
bae59e346c9ca51516556b59a612773b *man/figures/README-example-6.png
ccb64af3465b9a921a03a2e99573191c *man/figures/README-example-7.png
652678fdbcc7b88b1436bb683a99d192 *man/figures/README-example-8.png
ab2b94f0fd938db1175fa47bf0ad2c0f *man/figures/README-example-9.png
3aa239f5ba7ddee8a8f403f216c5a0a6 *man/figures/logo.png
7e7e52ac72de7aa94595d8f5e7cbf87d *man/fullSlope.Rd
db542eebda3abd09601a8e1a5fa8a0e9 *man/geneAnnotationPlot.Rd
575fa8ec53b355daf16a15ab528d210d *man/geneSearch.Rd
38fd0b9e35319ccc3f37f029fc536f00 *man/gffSample.Rd
fac4d434b2967fa80f4128b3e2e3044f *man/leftRightBlockTranslater.Rd
79b48a40fa42fb41619cf95eefec2126 *man/makeBlockPattern.Rd
3e83eccbb43d0034f13cc54a538cb31f *man/makeFullSlopes.Rd
706782219a8e9a98ee8eebe1f797ade9 *man/makeFullSlopesDirect.Rd
745d32a26b18047590d7fb6dfe913d51 *man/makeSlopesWStarts.Rd
eafd9a60a140c517117bc2877429c7bd *man/noPattern.Rd
94bb8de07fb69a2b12c101f5075a1756 *man/optimNoPattern.Rd
3b7f11953eda4c264132a30e34a365e2 *man/optimSlopeFull.Rd
601f4c7f156bf86b99af0d99f5fdcfa9 *man/optimSlopeWithStart.Rd
daed69ec8a3da05178109dcf400a59e7 *man/patternBuilder.Rd
69d6c09bc8aef288443317b3776a690a *man/patternMatchSize.Rd
16270e517cbb8470bc95f45bb1bcd947 *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
5c02e5991c2b20a7c233aaf54e962eb2 *man/slopeWithStart.Rd
c8b5b9916cc98f21c1ab95cdfe2299db *man/slopeWithStartDirect.Rd
72b26b953443bbb5fa13e369fc37efff *man/specTransductionPlot.Rd
4b1fccee7592389eb5fe747d774529b6 *man/specTransductionSearch.Rd
41888206ad27e624637e0c3ab2e4ea3a *man/specializedTransductionID.Rd
7907a3ef440638d71c1ba3c06b6f634e *man/zeroCountSearch.Rd
7a44d7d9a30b1442cbcd227b6fe1ed77 *vignettes/TrIdent-vignette.Rmd
