2d482c50f1779f0c6d8ae08f792d3bc4 *DESCRIPTION
3286b9dbd869f28fd0353e0f14b440cf *NAMESPACE
4f9b11088828eaa177d8a4812e77f8d3 *NEWS
3d9a4dc388f097b720b862a9b389aecd *R/BEAM.R
910a4bf1ae1f3d476ff1d58f28184011 *R/CellDataSet.R
e5517078177e1166b0c0a2e1d4b08843 *R/CellType.R
bc5b68d13890b5fa24f4c1ab78216bcd *R/CellTypeHierarchy.R
d0bbcea69d82a601eca3d7f481394f59 *R/RcppExports.R
588beac48aa77ac9e8b1b1bc8891e617 *R/cds_conversion.R
74652f34cbe842adc5caace0a68382d8 *R/clustering.R
d41d8cd98f00b204e9800998ecf8427e *R/data_sets.R
db0254ac3585d41892490066e7b1fdc6 *R/differential_expression.R
e917289761b596563c3db8f566847c53 *R/expr_models.R
5f77800fd7ff9d83b66a70bcffe893c7 *R/methods-CellDataSet.R
1dc8397225f7eb12dff9aab6c4391a4d *R/methods-CellTypeHierarchy.R
c4652332e1c011e28112fa8226cbd9b5 *R/normalization.R
8f34ec20ab968983d97458fa1c8a68f6 *R/order_cells.R
377b33625d191c6fe97399d36d98d91f *R/plotting.R
4e8d93d503742c099e64fb3f0a62453e *R/utils.R
e1b583b493cfcf78ed1f8ee1787d73e6 *README.md
c8dc3eea2ea7bbe604c3619b6320b0e8 *build/vignette.rds
918e70aacbfa2d27b600aae11b6dbd68 *data/spike_df.rda
77acdd3ec82c4ec910dcd0bbc9d53031 *examples/HSMM_analysis.R
1003efc56a533ebd36010b8069d27151 *inst/CITATION
38ffe7498ef73b14a339d7e2dbdd23d2 *inst/doc/monocle-vignette.R
4e30fabd4bb4650bfba26d61978543b0 *inst/doc/monocle-vignette.Rnw
71569e91589e0cc9e3cbbcfe526ea85a *inst/doc/monocle-vignette.pdf
9c7e577cf9d500d98a1cad2cb5461ecb *inst/extdata/lung_exprs_data.RData
f65ffe7cf61422fac87ea8b3350bea62 *inst/extdata/lung_feature_data.RData
2e462a7fa942eadbd5bb82078b903a7c *inst/extdata/lung_phenotype_data.RData
b5078e51410158c95f409b5e6c16b605 *inst/tests/basic_tests.R
50329a873fddcc4f1f1a6b00b3dd6fdd *inst/tests/test.addCellType.R
ae3e7bffcda8126de5092ae851cc1ea8 *inst/tests/test.calculateMarkerSpecificity.R
61eede7ad0e001ce6a2a3d76bd870d64 *inst/tests/test.classifyCells.R
754562527865cb9c06ce283c9f88fca1 *inst/tests/test.clusterCells.R
84195c78a454d03a782f4c3af8aace9b *inst/tests/test.detectGenes.R
d71a10e6214e133abd2116d4d994b1a3 *inst/tests/test.differentialGeneTest.R
9e7b3489c15cf0e7cfca941bc43a673b *inst/tests/test.dispersionTable.R
d77611d26068f12be13cdfc3d97e2a2d *inst/tests/test.estimateDispersions.R
a5e2fc1156a722e0a9cf51a575d0ef22 *inst/tests/test.markerDiffTable.R
01a0bb3a6f3b4e98616f185f5fb9b220 *inst/tests/test.newCellDataSet.R
95ec2ffa804c015695876ce9aa762d02 *inst/tests/test.newCellTypeHierarchy.R
b43a7f36f6aacb488868ef156d423f0a *inst/tests/test.orderCells.R
f636107f8b08a134268d6413525a3e49 *inst/tests/test.plotCellTrajectory.R
d1d78f98b4d214c11c6b25db13bac1ef *inst/tests/test.plot_cell_clusters.R
996e853fe8eed3282e6f8ff3c945a628 *inst/tests/test.plot_genes_jitter.R
2af73739a1a3cef182761c8563643361 *inst/tests/test.plot_ordering_genes.R
dd5e2868f8156a2e73f3facdfbbe341d *inst/tests/test.plot_pc_variance_explained.R
b118bf8f0e4fb9c30b1f981dcf4e22ff *inst/tests/test.reduceDimension.R
dd7827bfd34c8e2b62b1894ccd62b6cf *inst/tests/test.relative2abs.R
fbc82c293c7b408fd0ac9af4121f6356 *inst/tests/test.setOrderingFilter.R
99cb2f0d5d56b88a45623cbdcb92bc45 *man/BEAM.Rd
458f13e7ee18195cf008fef0ce8c7b61 *man/CellDataSet-methods.Rd
8dcab2315ddcae29a51099952e37ecb6 *man/CellDataSet.Rd
81dcf71fc9a6ec56073a17d9d6ed7440 *man/CellType.Rd
3ca42f0fb2ec37f0af16c44c85d3cb10 *man/CellTypeHierarchy.Rd
181829b054b07b858c29afb3e87d0f9f *man/addCellType.Rd
dfc7aa7736549189eceb6c182daede3b *man/branchTest.Rd
56c4ab4ca98f8c756922296100848717 *man/buildBranchCellDataSet.Rd
45c908ed9e535943f5fb5052f4a2c9a7 *man/calABCs.Rd
0562d21b149d8d0fc8303876894ed384 *man/calILRs.Rd
bcc16416f0444c881cc692c5c8922213 *man/calibrate_per_cell_total_proposal.Rd
90803adf61e35b39f2686f015acdf959 *man/cellPairwiseDistances-set.Rd
765e7a14ca8f842793852ae7060dad91 *man/cellPairwiseDistances.Rd
b679f37f14300920eef49e4afb9e91de *man/clusterCells.Rd
085114b8f304379691f2a07c998f3087 *man/clusterGenes.Rd
b121c157893768759d7614e99841d816 *man/compareModels.Rd
6f472ee73541a7caa7d25e643302c809 *man/detectBifurcationPoint.Rd
82783c192f545e7ca256311948d9428e *man/detectGenes.Rd
9cd00715e929b4294ce4aee49c31ed1a *man/diff_test_helper.Rd
99125462a183b9ad629df8dac94ad675 *man/differentialGeneTest.Rd
c4e77304bf5d890df122bd2afa8c092f *man/dispersionTable.Rd
ed6f23a5c8835d8e6158791e098e921d *man/estimateDispersionsForCellDataSet.Rd
9e48c83a009be7f7780ec8d15d423b24 *man/estimateSizeFactorsForMatrix.Rd
34a01172110138b9852b34bce5b5d1aa *man/estimate_t.Rd
cfc543ad5f9412e2d231c17d163aab07 *man/exportCDS.Rd
915ba83ed5056e6c6e4a72e2a8495b56 *man/extract_good_branched_ordering.Rd
0b802abcc0a9350246b167f26e3a6851 *man/fitModel.Rd
7e189d549e46d5817560496e34a6de69 *man/fit_model_helper.Rd
1e402fa7ed2737123ca8ab6be27199de *man/genSmoothCurveResiduals.Rd
c8e1a7902b8137aade952d69d24f4771 *man/genSmoothCurves.Rd
b549c02deb60c1314cb87569ae2a49cd *man/get_classic_muscle_markers.Rd
9d9cd1d2ee0b464a7dcfca63dbe0f74b *man/importCDS.Rd
6a6dddd16c607c06736f638d54bd7c62 *man/load_HSMM.Rd
6a92edd744b3ddfc3e74b518bb9f47ab *man/load_HSMM_markers.Rd
fe6c67404a36d00916f621f98ce2da72 *man/load_lung.Rd
4bed82e306de69d90bcaa1e9d3f7b870 *man/markerDiffTable.Rd
f9096b244c6c639ad0001e46a10d5bcc *man/mcesApply.Rd
a481e1ca2e607948b1a59db893973ad6 *man/minSpanningTree-set.Rd
7113a20737b11dee623a9518bd093c14 *man/minSpanningTree.Rd
debbaafc7ffd957ca01670ba0545c2b9 *man/newCellDataSet.Rd
28f0ef3703998d263489e0201069fd9f *man/newCellTypeHierarchy.Rd
fcb939ce25aebf15d23116a93ba04556 *man/orderCells.Rd
3ead39b1eef6908799649cf29a188ef4 *man/order_p_node.Rd
73662859b214e11f1c31d422c1802113 *man/package-deprecated.Rd
d8e279146953cec2d6b4d799529051c9 *man/plot_cell_clusters.Rd
fcbf4962abb9c458ab0a2b284acd0451 *man/plot_cell_trajectory.Rd
965c270e9d497bbfac916636fb82b270 *man/plot_clusters.Rd
1e0b5eb640e601d7db401a1f935c62c6 *man/plot_coexpression_matrix.Rd
e6411b6917849bdfa21b49ca9d9aa0d0 *man/plot_complex_cell_trajectory.Rd
f9f46a296492312ed1ca1e34e64b6e00 *man/plot_genes_branched_heatmap.Rd
a50fabb9d010f35262e9fa8dc63e7e52 *man/plot_genes_branched_pseudotime.Rd
2dbafd41fe422f78f5fcde32d0f146ab *man/plot_genes_in_pseudotime.Rd
5067a9ee40d426c7b48447e4469aa111 *man/plot_genes_jitter.Rd
14cac5d5beaf7a2b5d5c934c0748ff98 *man/plot_genes_positive_cells.Rd
310311a63a1f0b4369bbecdc87435259 *man/plot_genes_violin.Rd
d2f10536f4f889f177339402634ca5ed *man/plot_multiple_branches_heatmap.Rd
648f535c2439c6a6c50e926ed25d9a5e *man/plot_multiple_branches_pseudotime.Rd
54d3e644207c4b80f848dcacaa6ecdcb *man/plot_ordering_genes.Rd
8bb0a6efbe4ed88cc29d0bbd0fe17439 *man/plot_pc_variance_explained.Rd
1ae4711c6c4a99a0891fb11d0a0e3e48 *man/plot_pseudotime_heatmap.Rd
4de28162ec0a3287acf95694d14b2f22 *man/plot_rho_delta.Rd
d8d9121101df8b1c681e4480b8ce6222 *man/pq_helper.Rd
607e7c0db77fb035816403ecfe260afa *man/reduceDimension.Rd
93776d9723671d50ef5b793a54945d92 *man/reducedDimA-set.Rd
319e609eaa31ae2869c695f8d827cca9 *man/reducedDimA.Rd
b9c9f75549a12c627569a5f840adca4a *man/reducedDimK-set.Rd
a69ea0febfcb9a45bfda5b95baca6271 *man/reducedDimK.Rd
ef6cd7a57ad6759ade012b1fd51d32cd *man/reducedDimS-set.Rd
4e13c3b37502501ef9d209e44660f2ce *man/reducedDimS.Rd
deae88df092eca563f258e065eadf918 *man/reducedDimW-set.Rd
6f9d2daa28eb84c01876d84f321d3435 *man/reducedDimW.Rd
407f7377f932b53efe6517e748aebcb2 *man/relative2abs.Rd
97f58249082a6bd1ebac90696df368ec *man/residualMatrix.Rd
1f1d475e75e043d0e4a9a5c9defdbf8e *man/responseMatrix.Rd
ae2f0bfee2596fa3f0f5537d749db792 *man/selectTopMarkers.Rd
e2f6329b61321818f983c1fe1ac93410 *man/setOrderingFilter.Rd
eb02185ea37780af33c2888fb7531e21 *man/spike_df.Rd
276bbcdcc4c3bd672ccaafa5b1a37ec4 *man/vstExprs.Rd
c5e33be98d7fc44a38236bdc248c8c24 *src/RcppExports.cpp
d80071ff91f139b4a332e92cc41ea8e9 *src/clustering.cpp
f3a643848283e1b131a35164bdaac31c *tests/testthat.R
b5078e51410158c95f409b5e6c16b605 *tests/testthat/basic_tests.R
7d3f0caf5cb0f81d801374af2cc1e4c4 *tests/testthat/test.addCellType.R
4097d118b73aa560b5baef4506fd045a *tests/testthat/test.calculateMarkerSpecificity.R
8f738a38628a4ba20abec90b08cc5d8c *tests/testthat/test.classifyCells.R
02822572fb941c43fdd7d829ca41fc26 *tests/testthat/test.clusterCells.R
84195c78a454d03a782f4c3af8aace9b *tests/testthat/test.detectGenes.R
7c4785dd324d9cbbb6d43a589c59e0bf *tests/testthat/test.differentialGeneTest.R
9e7b3489c15cf0e7cfca941bc43a673b *tests/testthat/test.dispersionTable.R
d1dc13be7b22861f617aba764e84aa5c *tests/testthat/test.estimateDispersions.R
6a738ef009471288e88393b83a575bca *tests/testthat/test.markerDiffTable.R
01a0bb3a6f3b4e98616f185f5fb9b220 *tests/testthat/test.newCellDataSet.R
95ec2ffa804c015695876ce9aa762d02 *tests/testthat/test.newCellTypeHierarchy.R
331f1d6832f90f0aee51b3e94d76848a *tests/testthat/test.orderCells.R
b8b53187a8cd0b4b6071f1c509f026b0 *tests/testthat/test.plotCellTrajectory.R
946c10cf7db45e483224bd93b2614a2d *tests/testthat/test.plot_cell_clusters.R
670cfab6386c0a83f4993383313b369e *tests/testthat/test.plot_genes_jitter.R
a282e8cd7031a0acd59d784281f48e23 *tests/testthat/test.plot_ordering_genes.R
db5640469e53a618a291de78a6e24d8c *tests/testthat/test.plot_pc_variance_explained.R
ce5863ad207b45af89da6a6056a4a6f6 *tests/testthat/test.reduceDimension.R
7582040f42df0d1e7858d875510e0786 *tests/testthat/test.relative2abs.R
d343c162082845b7643eb49429f8d552 *tests/testthat/test.setOrderingFilter.R
7ec15c16d0d66790f28e90343c5434a3 *vignettes/framed.sty
b75d7fba8b77eb50364245650377ad00 *vignettes/monocle-vignette-knitr-concordance.tex
5344316029ff1ccd97cc59a9d18d54d1 *vignettes/monocle-vignette-knitr.pdf
996af0f4aa41c629ed9586d4e4eeea1f *vignettes/monocle-vignette-knitr.synctex.gz
cbc8b8ffd5d19b20091c30b2b02c85f5 *vignettes/monocle-vignette-knitr.tex
4e30fabd4bb4650bfba26d61978543b0 *vignettes/monocle-vignette.Rnw
c8b4df930e77775766b522e07efd1c20 *vignettes/monocle_alg.bib
ad10254d567ffd3ec90a4bb570c2d815 *vignettes/whbiocvignette.sty
