9524e65987728edd7ac948cdce3814c1 *DESCRIPTION
c70bcde77835ec1acb9e276d1a14523e *NAMESPACE
6be0bd6bb96259da4c4fb5d214569af5 *NEWS
51869fefe2e0ffc7d1b557d49d7add19 *R/MRcoefs.R
c614dd473d0ba2b64a736f23e2a5edab *R/MRexperiment2biom.R
3c7e8dd989510e6860723e759deebe0a *R/MRfulltable.R
0985fb80d2202165c6569c0aab7dd6ce *R/MRihw.R
da195f0198780a499b34b885757f74cc *R/MRtable.R
e597ed189168c2ad9c16986823ef2c15 *R/aggregateBySample.R
b958c9339fe86c9e603a60b1ccf05afc *R/aggregateByTaxonomy.R
0121c4b1642f46033020cc3a6baf70a2 *R/allClasses.R
4114aa51ba0f456b5dc39263fb6e4593 *R/biom2MRexperiment.R
48b279c5dede6e6dfd38c5bda0925fd2 *R/calculateEffectiveSamples.R
402af47f9f19496dd95e0571a4d028f6 *R/correlationTest.R
85cd56f9e7e294e91f3becc34f029547 *R/cumNorm.R
ceb8a9fabc2b5afbd1421d8eaefdf39b *R/cumNormMat.R
c10f593185ecc673e4dd2f18b2a73b0e *R/cumNormStat.R
63aa9ea28ace989c73e16195292e708d *R/cumNormStatFast.R
712c81d47b82b55e2acb8f0701a71e37 *R/deprecated_metagenomeSeq_function.R
a8c646b7a3430746c7719c4a09c2d7d5 *R/doCountMStep.R
bbdc5c7f718b70ce52a212a2530b5ecc *R/doEStep.R
ee2a41e576486aa1001c540cc34a1b31 *R/doZeroMStep.R
4d9ffa7a94ba3b2460f99ede0e252a15 *R/exportMat.R
658680419e41332721f4a9fd6a4b2074 *R/exportStats.R
e0c4c1796cfe745d7eb9880fd687f041 *R/filterData.R
4af5c2c189c382dc4bc82b7bc35cdae3 *R/fitDO.R
acc2ebd545846d0dc4f6bb8a353a20da *R/fitFeatureModel.R
c01baad18ce4755f8319b4b44c1f5e6d *R/fitLogNormal.R
04a695a73e879cb3d8c3dfe345e2bc06 *R/fitPA.R
f624b0ac07d14a3fa0aa3287799c63f9 *R/fitTimeSeries.R
9cfb8688bd3308d575b1ef2e4680f31a *R/fitZeroLogNormal.R
bc5cf37a00b51190f3a55227cd2c7ea6 *R/fitZig.R
181b35f7e1cce3668e6933e9596efd38 *R/getCountDensity.R
e156f7a40ae21c4411a83829ff2d6b8d *R/getEpsilon.R
88dc0ee387475d1b4e74740d1ee0c6ff *R/getNegativeLogLikelihoods.R
ea0cf2a204273ebb101596b22b89a169 *R/getPi.R
70fbd2c926c3aeaa17bbfaf22ddf94e7 *R/getZ.R
ede263e53be42c0e0cff3f638d817a3c *R/isItStillActive.R
725aefce87179e578b4e5e8bcf36ecff *R/loadBiom.R
7ac15fe0242ac89298709cd431b32fbf *R/loadMeta.R
7cfdfd5152b4622a90a8b2f006ff6d46 *R/loadMetaQ.R
162253eb9af7d3ece168a537e6d4611f *R/loadPhenoData.R
e4b198c5d01526b041b000135d39065b *R/mergeMRexperiments.R
699787eda117fe23ee3c725299ad4887 *R/misc.R
a72f4a92906f5e188012bcd383b7b63f *R/plotBubble.R
1d9b988fc584ff6b674d2b2cb74466fb *R/plotCorr.R
75cb1fbfc6f2264a145afe269b0bfb7f *R/plotFeature.R
59c82956741eb524669c189344700452 *R/plotGenus.R
e3f7b29aeb898956f7032bdc90c1fc31 *R/plotMRheatmap.R
b0f5a67030728586115b55f1728ea236 *R/plotOTU.R
5709633efd4b879fead8abdb9939c059 *R/plotOrd.R
eda5dae29b830f26677763a3159ac62d *R/plotRare.R
f2ec7b52cb52823670754cfe6ce17db0 *R/wrenchNorm.R
606272eead308474b366dadd0ab207d6 *R/zigControl.R
564a3609fbe1c3f018f02d102ce18118 *README.md
c1ec5ac246088748c245db50620515bd *build/vignette.rds
f4f3068763172b97eb14a2d04ab0d2c3 *data/lungData.rda
678ad9d8d67a56529ead43ec675694a9 *data/mouseData.rda
74e93a154752b86db625616f5439348e *inst/CITATION
b2dad218662be5b555d392782d934018 *inst/Dockerfile
043aeeb47fde03c5d24fad0d47234ae1 *inst/doc/fitTimeSeries.R
8ba09526b340276b4ef8f8e62ddd003b *inst/doc/fitTimeSeries.Rnw
fbc90d17dc7a45a68147c1c1425ccc63 *inst/doc/fitTimeSeries.pdf
4ddea39627beab04cfb61cdfcc40a86d *inst/doc/metagenomeSeq.R
3dddd858fa50e3ad7696ee15570ce539 *inst/doc/metagenomeSeq.Rnw
e3f7fec63d540bbe3a78b67fa42a8c58 *inst/doc/metagenomeSeq.pdf
4adc00f2103f333dbff448eed5c0b726 *inst/extdata/CHK_NAME.otus.count.csv
f28db26b3ef19f17f21aa0f84dd4b616 *inst/extdata/CHK_clinical.csv
df200bf279bdca766a43c937b6156ce4 *inst/extdata/CHK_otus.taxonomy.csv
aae860fe41ff6c976324c42cc5633baa *inst/extdata/lungfit.rds
4f047b91674dd0fffe344f858be20022 *man/MRcoefs.Rd
8bf235dc5a9ddee5d0737b13a93154ea *man/MRcounts.Rd
7d0a6f4a8be148e583feb7fce2503014 *man/MRexperiment-class.Rd
98a5f4130d47ad63ad4b287ac9099441 *man/MRexperiment2biom.Rd
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9d798fda119723affe04abd052b380a4 *man/MRihw-fitFeatureModelResults.Rd
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7a3da4755f0d435b6e40befd815d5c72 *man/MRtable.Rd
24ebb618b865e3b3c913a8761ae00983 *man/aggregateBySample.Rd
b9fdeae940540856489259caa26cc755 *man/aggregateByTaxonomy.Rd
602d31c9907d5c3eef52ed3c0f9310ba *man/biom2MRexperiment.Rd
f4ed2a60b40abf13b62331af88486aaa *man/calcNormFactors.Rd
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3b2231e71bc2e5c73250e1a2f19372cc *man/calcShrinkParameters.Rd
eea5e93d9c47e97152cbd63cfbcdb168 *man/calcStandardError.Rd
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ea9f741548ec5e29ec5e21f86d69f8e4 *man/calcZeroComponent.Rd
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0afcd8875bb2b77f6afeb684eff2c3a7 *man/correlationTest.Rd
c0b02d2a1568c6804064f876f85d3eda *man/cumNorm.Rd
6a38652d2a160a82da7c5797344b2c05 *man/cumNormMat.Rd
b116daf96b00835f14cdfeecf7d8671a *man/cumNormStat.Rd
65ca559797d79a42900dab856fc4c809 *man/cumNormStatFast.Rd
e0984a2f59976064699110bc62a40d9d *man/doCountMStep.Rd
e778262726db6bcdd45f66d03b871336 *man/doEStep.Rd
42476bcd07a7701a656e4a4fca2e8fe5 *man/doZeroMStep.Rd
a475460d9de7f5585dbb05d8e3365031 *man/expSummary.Rd
fbc8d195e8c102a5c02564f85632a7f5 *man/exportMat.Rd
8a95d6f7b9f9eda72abfdc50f80106d8 *man/exportStats.Rd
7a445e6a35216eef6407507285040376 *man/extractMR.Rd
e7696af40c35d9b4722e7e350edf88f9 *man/filterData.Rd
1041b98058621e394392d8393c3b93a5 *man/fitDO.Rd
1bd614bf5490d5a2fdfb5613625d6b1d *man/fitFeatureModel.Rd
8f4dd8c3484e9b9557022c29fc4d1b82 *man/fitFeatureModelResults-class.Rd
b7e1d9b6d13ea588e6a8e1e50dddfda4 *man/fitLogNormal.Rd
1b02b549438afee328121642a93f4d67 *man/fitMultipleTimeSeries.Rd
c7e4b67313856f1110ae44526f589c21 *man/fitPA.Rd
bea3231bd0a8a3c630fe3a42c2c5689f *man/fitSSTimeSeries.Rd
8b20521dbaec5d42bd54e05d39da33f9 *man/fitTimeSeries.Rd
cc08972fb99469aa42d9791a4049b635 *man/fitZeroLogNormal.Rd
d88c2f76c6a2f20f051473c22e3d0a38 *man/fitZig.Rd
fcb56328b6d3c96fdeb8f562cbd88bf8 *man/fitZigResults-class.Rd
f0a401852ec1676c3681a9357f4b207f *man/getCountDensity.Rd
287542c20061270d0e4d9c522b746c47 *man/getEpsilon.Rd
8eb608f28b99f61e21832612e1104df4 *man/getNegativeLogLikelihoods.Rd
4364f756a9ac5b8e57bc79bb8b5ff533 *man/getPi.Rd
18507b605ee4b67e662e52c6d3d526aa *man/getZ.Rd
021801f95b5757e4509c4d9ba2355187 *man/isItStillActive.Rd
634933e16c50075ad2348e044592fa18 *man/libSize-set.Rd
b7e25936414a0f6fcaa2efc8b9f8fcc8 *man/libSize.Rd
ae29d7d068dfc71b75d229990c27fa57 *man/loadBiom.Rd
a58bef11f0b5abb70d74c865f0ab7f89 *man/loadMeta.Rd
f89d36c22b40efdc5735068906d97c7a *man/loadMetaQ.Rd
3c16c6bc43dac6abc0e496d314e96e98 *man/loadPhenoData.Rd
f4b1a20710b25d77586ffe4c44cfdd82 *man/lungData.Rd
49515287afdc87026903e5437797bad4 *man/makeLabels.Rd
1257bfa4a29288b321af2f6b466e2de9 *man/mergeMRexperiments.Rd
dd9f481c2e9c64fd1e61dd2c6b0151a2 *man/mergeTable.Rd
82b095ecb1ee394e0ffcf23ed84ba70f *man/metagenomeSeq-deprecated.Rd
842808c19e007869d7fdfbb53f7937a0 *man/metagenomeSeq-package.Rd
1ac0ade49e2a1cc67e61d806ee666510 *man/mouseData.Rd
a7a689cdbf54467c139bf7e7f8b48657 *man/newMRexperiment.Rd
fbab7e2e8d2cbe0d06ba539440523d0c *man/normFactors-set.Rd
6075a16c52ee84100d0c92fbd1368ad3 *man/normFactors.Rd
f91dfd514072496a04048b15b36d3379 *man/plotBubble.Rd
a20443b7aa883164d6919648ca98e1b3 *man/plotClassTimeSeries.Rd
499d2197b7f8857b1ef1bf7f6eb8143f *man/plotCorr.Rd
a6a6a53e5996caf22fa051a45a08ed7c *man/plotFeature.Rd
34ff3b8b69d3908a344ce2af09136846 *man/plotGenus.Rd
c266a5ea9ec1cd4c02bfc17feed8d500 *man/plotMRheatmap.Rd
f795c5b4c6ecdb4adc91770d15100461 *man/plotOTU.Rd
9c45076918714b3e8f9139f68f142ec9 *man/plotOrd.Rd
59ffbaaef583a06eac13f7299ef562c2 *man/plotRare.Rd
95961c000df23df30d5c7affba8cfb45 *man/plotTimeSeries.Rd
0530777d0aafc539fa23900a06a12717 *man/posteriorProbs.Rd
7942240b1da2a3683404f1b080c21f5d *man/returnAppropriateObj.Rd
dad91976dc815e9a507801a2b74a4c63 *man/ssFit.Rd
e960986a574734deecce5e3b7d34ec70 *man/ssIntervalCandidate.Rd
fdeaccb02e6296cc644b41b8fe4bb13a *man/ssPerm.Rd
0e7d6787c205b3cd07ce235c916e4dad *man/ssPermAnalysis.Rd
b2975a22ba55bd5523b21e08fdc867a9 *man/trapz.Rd
1ad46d00eff4e9e6dbabcfdbf93f28e6 *man/ts2MRexperiment.Rd
d39b7340ecb529acdde2ca32e7891fd5 *man/uniqueFeatures.Rd
7ba28bf7585b6b13be68bc9ec4e26111 *man/wrenchNorm.Rd
73aec95cf14ea2f964c3fdb6150ad0ef *man/zigControl.Rd
dc1ddba3636ea8bfd2bd6c4c6da9b034 *tests/testthat.R
4f643a6eda37eff4ace81c51ed863c41 *tests/testthat/test-fitZig.R
a8bf8ea4e6613394bde428547ef9cc6f *tests/testthat/test-norm.R
f39a84fc37b79bfb18227c7cb5809ace *tests/testthat/test-wrenchNorm.R
8ba09526b340276b4ef8f8e62ddd003b *vignettes/fitTimeSeries.Rnw
e2245331407faf57a75775e563c42573 *vignettes/fitTimeSeries.bib
3dddd858fa50e3ad7696ee15570ce539 *vignettes/metagenomeSeq.Rnw
21e615bc616407bece667ada9bb13b6f *vignettes/metagenomeSeq.bib
d8278b552cab2d0bf32652b99a96974f *vignettes/metagenomeSeq_figure1.png
ebd30b8892f7867d2ce1bd7614718e3b *vignettes/metagenomeSeq_figure2.png
88866dace9b4330ac9cf728c55dceb88 *vignettes/overview.pdf
