df52565ebe582802f55899491bf5e223 *DESCRIPTION
84dcc94da3adb52b53ae4fa38fe49e5d *LICENSE
5ff6f7fee9859c1e154b612ab5653f23 *NAMESPACE
22a049560c4b20f7e73f3efcfb9cd8e2 *NEWS.md
5946f9b2709269c44b6253fe33edd0b4 *R/RcppExports.R
ea3c8a20ca91537cc5f3b3d4acd77941 *R/clustering.R
f59dbb77d43c00c958fb3828bc1ae3cf *R/convenience.R
135f7870b28fc7b351b825e3bb7f1f63 *R/data.R
abcf24b26367a8854734ff0736630092 *R/differential_expression.R
b1e5cc17d735d89e11dc6a137d7fe50a *R/dimensional_reduction.R
366be82b7e21d898bbc7ba9eab719972 *R/generics.R
b65a625ed544c7432a5604fc5584c8e5 *R/integration.R
3544396654c2b5b7d3bb72ee28513e9c *R/objects.R
361bb25e04c1296de2cb7fde91156027 *R/preprocessing.R
f42f9a3b70240d856aae9f1cfd214188 *R/tree.R
935f151d4b889a379fbefb7e7395ed66 *R/utilities.R
6bf6011a263d20429979ad1db33f12dc *R/visualization.R
248b1a13e13438213458a218a535de65 *R/zzz.R
74262d0f2b3f62e9beabb2d9146d314b *README.md
e84661f995a9f29d1a09ebcdc27d3a82 *data/cc.genes.rda
f31fc6d89626ed493ef21557a33021ac *data/pbmc_small.rda
f8e3f10318a2bc7bed0d5db84022376e *inst/CITATION
d07fe4eee5c09cc44e96c17e683cb10e *inst/extdata/pbmc_raw.txt
3b5829d7c21d05ecb1290ab8e03c8263 *man/ALRAChooseKPlot.Rd
9144bcea7f7cfdb3014db72584bc0068 *man/AddMetaData.Rd
77ea5a83ae3ea07896b65eb18de67cd2 *man/AddModuleScore.Rd
7f4dede167c0b2ecc2b9e952e15ee3ab *man/AnchorSet-class.Rd
4e893b36fe1668e4d95200e6b96a29bb *man/Assay-class.Rd
afa2ca7ee28cdc822add9aebf459f253 *man/AugmentPlot.Rd
ca5dadeedb16b6b85526eb1de63dd7a3 *man/AverageExpression.Rd
d9558f568959bfbd8024fb63642bc61e *man/BarcodeInflectionsPlot.Rd
38b9cdbe2af8639eda75846b2c385847 *man/BuildClusterTree.Rd
baf632d70fb6355db716b38128ab041b *man/CalculateBarcodeInflections.Rd
8ce765eeaa066c7a1d57dd3b5dcdf366 *man/CaseMatch.Rd
4e18172afe16aefbf5ab52a0c68408de *man/CellCycleScoring.Rd
80bc40d33ecdae8d86d70f0e98abca5a *man/CellScatter.Rd
295a7d839185b68bf925e77fa58501ca *man/CellSelector.Rd
dacda2e4537d0e4235380a301153c6be *man/Cells.Rd
bdba5720fb1499348be8b1aeb0f8ea9d *man/CollapseSpeciesExpressionMatrix.Rd
e734784435ce40c180fb4519126c20fb *man/CombinePlots.Rd
48df91074760789c3bf9285b472303b2 *man/Command.Rd
daeebf2d27175e0dc2686b7be75c8767 *man/CreateAssayObject.Rd
747d045961405a6f23b1ae94430ef9ed *man/CreateDimReducObject.Rd
85a8ef27b4632fe2e5907853c0bf9df7 *man/CreateGeneActivityMatrix.Rd
6e87c48fc96d836d2cdc8f91a2daf76d *man/CreateSeuratObject.Rd
ed3cf6431b7ae74072711f5cdceea03e *man/CustomDistance.Rd
f00401ae93dbb69d80ba0e187b8d75fe *man/CustomPalette.Rd
fd5832a9ae61cd5b5d47b9340d1fec59 *man/DefaultAssay.Rd
a0fd7b27ab535a13f9e821d515442369 *man/DietSeurat.Rd
c6e6034b2e18866bf45720d3e9f7892b *man/DimHeatmap.Rd
fb66cff65a34e3b8689c9bf0bb0a9e59 *man/DimPlot.Rd
49423f39e8f03105479bd722390b841d *man/DimReduc-class.Rd
8f0e6c45196e3134360d441a211475e1 *man/DoHeatmap.Rd
cb4cae2f9679f3cc1bf3a19dbbf9559e *man/DotPlot.Rd
7f990b57af606c619cd32fc4823df3ba *man/ElbowPlot.Rd
2a9ff1776069af7481ae99b98ccd44ea *man/Embeddings.Rd
883af2a01a9cf232e6a771172fb2f9bb *man/ExpMean.Rd
f135b57ab61fdc61c872995c053aee5f *man/ExpSD.Rd
e5f8196d5bf616784532f3b91fc35b9b *man/ExpVar.Rd
9897848fd9e650cc4512b3850b913c1a *man/ExportToCellbrowser.Rd
c764294bb174f7eae8807fd0e1089b7d *man/FeaturePlot.Rd
9e55c18eb26d75284d6efebe81d83b03 *man/FeatureScatter.Rd
6aa7b60217d27dcb3269a78aa8157794 *man/FetchData.Rd
82abceaa6885fcc4330a16d00445e404 *man/FindAllMarkers.Rd
4dd53b4d927bee9ff2b3ba0cac2e17db *man/FindClusters.Rd
3efb7242a14127d0bfc2876e60163761 *man/FindConservedMarkers.Rd
36a05aff50f77e9e55e4f10594f897ed *man/FindIntegrationAnchors.Rd
9f92837506273ad5faf0fc3fe4c48b3c *man/FindMarkers.Rd
ba1167914146a3923485a155d692aa3b *man/FindNeighbors.Rd
eb2b71853de3ce9a1076b5d25c1b1e35 *man/FindTransferAnchors.Rd
c84cb00416b6ecdbecbfdbd93034e525 *man/FindVariableFeatures.Rd
0510c94030d8033d795243dcea889310 *man/GetAssay.Rd
4b28e1ae9e34d811ba9b93a434f82cb6 *man/GetAssayData.Rd
8c67742b1850e245dabeb0080496092d *man/GetIntegrationData.Rd
c7ad5a244ba571fb110e5643ecf12d06 *man/GetResidual.Rd
04c6af6f3b8c9afd0917a1cc39f412ee *man/Graph-class.Rd
b3c9475faf735f129a54086a6db84e81 *man/HTODemux.Rd
22d9bf2230f255527751938770ebb24e *man/HTOHeatmap.Rd
53f2d89db6704aee338808677c429edc *man/HVFInfo.Rd
e342e4ec0066bf6139aefd02ea29f90e *man/HoverLocator.Rd
8fc5372fec49440c613af10f47a8219e *man/Idents.Rd
e3656513a6f11c5abae999202aef1804 *man/IntegrateData.Rd
f07f85f35c068862949ba8aea6a7d0c2 *man/IntegrationData-class.Rd
b577e19ed30fed4dad88521ee8bb5f3a *man/JS.Rd
1bb33c39e65d75006d3465938447ff10 *man/JackStraw.Rd
7032df72bd3bc5bf505aeb5404ebe736 *man/JackStrawData-class.Rd
42f16a7803d74fbbeee01c143f7e9fbc *man/JackStrawPlot.Rd
419378df10e1776c68fc8cac800442e0 *man/Key.Rd
ec6e773d7bccd1b7fac4f4f775b8434f *man/L2CCA.Rd
7d827c4056462d47b10ee51135b81a28 *man/L2Dim.Rd
e016f32e58314ab47c4ee8ffd4fb651c *man/LabelClusters.Rd
4b737e7922d736086fde965d82f1b8ea *man/LabelPoints.Rd
71205aaa6d7a80bad4dc684ea71353c8 *man/Loadings.Rd
2b5568714b2d74201e43357a8fa73c8c *man/LocalStruct.Rd
754647438aabcc6aeb541e1275f0b501 *man/LogNormalize.Rd
6abf43f5649e3dc037f802111fb92f00 *man/LogSeuratCommand.Rd
be6f87856e0864243fe230d258bb3b96 *man/LogVMR.Rd
be1bc91b26c1d752f339fd392edfd55b *man/MULTIseqDemux.Rd
f2d0fd17c466df6cfdb625403fd52550 *man/MetaFeature.Rd
ad9c49b3faf112a1882eb0c009547070 *man/MinMax.Rd
d096fdd966337afb93c9bf5253d791c3 *man/Misc.Rd
02fe542af69275237181c12b794d8bea *man/MixingMetric.Rd
6bbe47f5caceaa1ab69638ec33145719 *man/NormalizeData.Rd
00299f524f6f209b605e4e1df4e4c63e *man/OldWhichCells.Rd
57a687ecf02de4e575ed5450a879458c *man/PCASigGenes.Rd
e7bd17eb4c60b884a3e077a092918851 *man/PercentageFeatureSet.Rd
c472a070ae7e3777ebc2c400455b98b2 *man/PlotClusterTree.Rd
c8f05fd9e49dcf85d0d35cf293244fbe *man/PolyDimPlot.Rd
f049db3279fe25e6d089e8cc735967a1 *man/PolyFeaturePlot.Rd
803758cb5762fbe127063d8b089bcc1f *man/Project.Rd
9e593940c8a6070f47c4f14359109391 *man/ProjectDim.Rd
bbdfbcfd18329e0adca953a727edcbb7 *man/Read10X.Rd
bfa85204a7e639af961c8b0dc32f5309 *man/Read10X_h5.Rd
56bb82d14a62ba66da1a59c49d11b08e *man/ReadAlevin.Rd
b56201e48e7bac211cf4554073c5a05f *man/ReadAlevinCsv.Rd
14e4ad476c6c3464abbb0c7188b6a206 *man/RelativeCounts.Rd
3265429dafe80a2e393401a1d6446c6a *man/RenameCells.Rd
fe2b1a2d8bf2a6fbd740798dfba2f0a8 *man/RidgePlot.Rd
528d50b054b1c8bc21ed59680b75994b *man/RunALRA.Rd
46e2232a6d8cc3b9e0fc55f15f3a5f3c *man/RunCCA.Rd
ce9d9ebf747a9dcc1082fca5ab9e6327 *man/RunICA.Rd
d2724699634b475beb976eb9e8d41283 *man/RunLSI.Rd
33f05231ec16f2351d5e0c64b885879a *man/RunPCA.Rd
ba97ec35275b8abbf2411e573e9b4205 *man/RunTSNE.Rd
4a96f5cc9503f75c3aa2961b8d8530e5 *man/RunUMAP.Rd
af4059e057151f5c58cde35f3dbbe1fd *man/SCTransform.Rd
b92204c9406eb253e2e2cb4f6e980cfe *man/SampleUMI.Rd
f603c7b5f39e6b727f47691ac7eca919 *man/ScaleData.Rd
45b232b3f8621ccaa9e8f3a1c4a0ce9a *man/ScoreJackStraw.Rd
665d7ecf2fc6bd3c1990033af903bf0a *man/SelectIntegrationFeatures.Rd
be8f994eb422be0acf9ce466ad295192 *man/SetAssayData.Rd
1029e6a8f77a5bec3f1272a5b6c8579c *man/SetIntegrationData.Rd
749dfea6bc4fd4f973cc03ffda8d1327 *man/Seurat-class.Rd
d9927e255a730a3822cd789bab0d6920 *man/Seurat-package.Rd
569f3e2abfc497ac3a035652d4611925 *man/SeuratCommand-class.Rd
c9198b8ff2093aa02b0ccc7cda1a9d2c *man/SeuratTheme.Rd
1e3bd590b07f93c9d2ce9f47a234ea8e *man/SplitObject.Rd
10b4efde5824a0eb4a845660b82728f1 *man/Stdev.Rd
0b56a6fe26123ba2c87ca93ca0a3d12e *man/StopCellbrowser.Rd
795c05a5f6b0d4330dc4245749aa87b0 *man/SubsetByBarcodeInflections.Rd
1d1e2027cf8168e3d9a984bbbe6d3c25 *man/SubsetData.Rd
3cf18a0619327727b30e4eca0fbbf98d *man/TF.IDF.Rd
79b32637ea153b3f68bfc99e5144e7e7 *man/Tool.Rd
baadd91d4ee8241049cd91da75fdb979 *man/TopCells.Rd
37e235afc083f506ca29c1102a3a11a0 *man/TopFeatures.Rd
66df8ab60bafc91e83c13e0add11816f *man/TransferData.Rd
a6dd88aeb59cc35bc0c499faef6f8245 *man/UpdateSeuratObject.Rd
f51c1f44c92c8ded4b390f12f4edf3b2 *man/VariableFeaturePlot.Rd
446f6011aae6d9623ea4d908226e0f00 *man/VariableFeatures.Rd
1fbf4accdf190098062d0699f2737a21 *man/VizDimLoadings.Rd
6448eee245dcd3ff830216684294effb *man/VlnPlot.Rd
687d54a0726024da0b81273b1bf9d915 *man/WhichCells.Rd
7ee1c557a525878f1fa578050c020573 *man/as.CellDataSet.Rd
186e2c44f694fe115062f3e4058c509a *man/as.Graph.Rd
0310637bd6a0903e8cb12a652697b72d *man/as.Seurat.Rd
dc04bab144868edf9e3011883f9b34df *man/as.SingleCellExperiment.Rd
29fa8aad68535bd377eb6ec5cf4489b4 *man/as.list.SeuratCommand.Rd
fd6331f875bb46a642030c746c1bb7d3 *man/as.loom.Rd
2cfb8cf87c9a2a7a8687e028009ef64c *man/as.sparse.Rd
e2f9713bf96350058cd4826c4762f677 *man/cc.genes.Rd
5b49fe595cbc7fc01655e6a25905d94b *man/h5ad.Rd
0c3cc3d5cc430fe3d2ba0bd551925d3c *man/merge.Seurat.Rd
c83eba96209207d78ce66966a6d92d8e *man/oldseurat-class.Rd
0f3b06eb038b97d59d556450bd7e9eda *man/pbmc_small.Rd
4a170c7c930e51911e90e2d5c8a9ccb0 *man/print.DimReduc.Rd
c763f46840237af8ca2821ef1e167eda *man/subset.Seurat.Rd
e3d3cb360fbfdb3c6974e14eb5f09870 *src/Makevars
2d00bfb3d70dd902867ef8b93b77ac43 *src/ModularityOptimizer.cpp
fa50cfd47c172ecdbb147c0958a068a4 *src/ModularityOptimizer.h
6b14b655eade640931673c1cc1357a6c *src/RModularityOptimizer.cpp
3604df6f0cdea7ccdf199b6f27413c0e *src/RcppExports.cpp
f193166041feebe599bebec19de3a92c *src/data_manipulation.cpp
6233a5afec8b4279616d2e3392a07752 *src/data_manipulation.h
efdafe6d860a47a3c5ed9642846eb009 *src/integration.cpp
d03bd7b8e78939ba29e8f31697e3fc48 *src/integration.h
fa46a78e09a6479196ef7a4bcc0ee0b9 *src/snn.cpp
694a8ab034ccab2c5f7c35bf47b3469e *src/snn.h
1d5009992bb3e703bb3f2482f9b8ddd2 *tests/testdata/barcodes.tsv
d2554fb8e4d5af543605d0a729e36109 *tests/testdata/cr3.0/barcodes.tsv.gz
70e1ed4c347e2563a90fd2144f375a26 *tests/testdata/cr3.0/features.tsv.gz
75dc5f8ba97f4c3bc30ceb7926c5759b *tests/testdata/cr3.0/matrix.mtx.gz
91aa47aeda59ef6d82105100a09d1497 *tests/testdata/genes.tsv
6693f4ae1a15e0985ed513ee83fad927 *tests/testdata/matrix.mtx
646ac9cb85813dbe838d804f78f717a4 *tests/testdata/nbt_small.Rdata
34b405818933dc96aac3fcd6594b483b *tests/testthat.R
e0da28fead6ff190a3128b444f49a43d *tests/testthat/test_data_manipulation.R
723ee1d34ca4174358fb8fffb1236139 *tests/testthat/test_differential_expression.R
af1fd8c0a7ca62043adcd34933211e16 *tests/testthat/test_dimensional_reduction.R
84a1a4b716c9f780c4daef3357fcec73 *tests/testthat/test_load_10X.R
e096ae1c8e0ea82b43c0e5ff4c5ba116 *tests/testthat/test_modularity_optimizer.R
5270dd5df9f9c5e8ffa1e8106c682508 *tests/testthat/test_objects.R
e472acdab1782bfbadb264693a0406df *tests/testthat/test_preprocessing.R
