92203db4afb4d6b1f53328a3c81d9dc9 *DESCRIPTION
3cbc2bf98b3513c50f88796bff408b55 *NAMESPACE
b34c4ee430f316d322065a9f587ad2a8 *NEWS.md
c3776170502abf5da43869e3a30f759f *R/ATAC.R
1c679e00369b10a6bc67e39184a94243 *R/DEG_marker.R
263c4a101fabda184ae09e183df52937 *R/DoubletFinder.R
71cdba76c163db11a0277f2d0a7997a6 *R/GSEA.R
3ec83c547d5aa0240727975f8e882d0d *R/RcppExports.R
db9420d196ad9bee62b92352fb9d9430 *R/aaa.R
c577269e89a430d38cdcb43d3e9d0132 *R/archive.R
a057ceffd784bffa6edb56cc71a25821 *R/cINMF.R
3dd4e141590c9456de4a570567180382 *R/classConversion.R
8bec61252daaf59073501b4fc12764a8 *R/classes.R
f7fb87af66caac959036c85b97538385 *R/clustering.R
a8d07fe19ee85d41e9fa379593f6d080 *R/data.R
0b35f08026f72a8f8430cf15c743f104 *R/deprecated.R
ff4603e40e87d2d3afb7a22557653744 *R/dotplot.R
e74ac6d00ac44c7481dcaaef51c7d848 *R/downsample.R
796e7797a5fe9b146afea7a62ea75563 *R/embedding.R
a1a27e02fc8fe61b1809f55a32e1afe3 *R/factorMarker.R
d3d8db03616af793c10040a4ec962e83 *R/generics.R
11c4282c3837c323cdbc154c441ded7c *R/ggplotting.R
9eb6e3ce7917c47403a47c3ec9903c7d *R/h5Utility.R
8e0da7d285f75fc9204f6dafcc4e4a62 *R/heatmap.R
8f796c462519165ab8827755fe560237 *R/import.R
9b247c57b3dc3f143edcbc35b287a0d6 *R/integration.R
1a4402e7c9d862a3720686f8aef80ce6 *R/liger-methods.R
868c006ce690402f4977652454cdec10 *R/ligerCommand_relates.R
0c0ee418ea9c5ca84dd9ee8e38117147 *R/ligerDataset-methods.R
596126930649f6ee92092f0c0f83860b *R/ligerDataset_subclass-methods.R
dde11a743b6ded944b9efd6f4de30359 *R/mergeObject.R
8a2879a5b55fa45c631f194ff18a4e81 *R/optimizeNewParam.R
04b4bfdf7fd65f8f79a2a7534fbf83df *R/preprocess.R
d7a54580ba6b0c63cf4b2782267b6f43 *R/rliger-package.R
3b5fababdb60c6d61152036532e7a063 *R/subsetObject.R
bb33f50b816b592b6d1bb4e95fb93873 *R/util.R
27e8db1404a99fd02a457495622ec643 *R/visualization.R
0d675ebc8a0cae8f4456890a475d7f7a *README.md
aa5e5a2cbfaea3d9b6cdbe378ac48cee *build/partial.rdb
21492a364f998f13e4d94e256305f28f *build/vignette.rds
5cae1eab838da773bfcf6c76cbcf099d *data/bmmc.rda
319a8e022f94e15f70422ca55b67da06 *data/deg.marker.rda
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96d5bf04243314c34c8688cb9e56deac *data/pbmc.rda
f7e24943e840a5d1957d37f38adac05f *data/pbmcPlot.rda
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cb537dd5167779db5505887817f5c076 *inst/doc/liger_vignette.Rmd
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1275dc6a1dfd2e4ef7291cf28825eb6d *inst/extdata/ligerToH5AD.R
a5f1b28304910d164707213e31054675 *inst/extdata/stim.h5
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8a741fa3eab4f90e420e704760850ef2 *man/alignFactors.Rd
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82658feb51771663047ed3b27d6fad91 *man/as.ligerDataset.Rd
9bb0848b925d4afe1b38e40706785efc *man/bmmc.Rd
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9edec1c0c8eacafe0aedb01129e5f666 *man/calcAgreement.Rd
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cc2b32db653270f79871095445dc07bf *man/calcNMI.Rd
384e29d71b4f4c41eca6f4730b42d69c *man/calcPurity.Rd
d5f7bdaa35173e3d2332ce2c6be67c8c *man/centroidAlign.Rd
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8998ab62a8fa73414e97459463e60983 *man/commandDiff.Rd
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63264137d2bd2df7410ec79a2d4625dd *man/coordinate.Rd
301d5509dfba30bf8e4d6bf4ed7cf9b0 *man/createH5LigerDataset.Rd
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d87fd9aa465945819d02093baaf2779b *man/createLigerDataset.Rd
3aabf3ce738a17947e8facf23a3fc4b6 *man/deg.marker.Rd
65c6ae185267fc526ee86c03b5f99dc4 *man/deg.pw.Rd
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6aba44ce2cf18d1c3a31836a83ceb30a *man/getProportionMito.Rd
a28f3e6bab1631a0c79caac644ce2440 *man/importVignetteData.Rd
224827cae72216dcbd3bb0eb79829c13 *man/imputeKNN.Rd
d06f3de7c9d9d07790d9391bd1000d07 *man/is.newLiger.Rd
7a83dd94560b3ecb9fea2bd1ca453059 *man/isH5Liger.Rd
3127173ee14e93510a80855226adaf29 *man/liger-DEG.Rd
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3439cd2c5a7c4213018e1d1342352476 *man/ligerATACDataset-class.Rd
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d1c35ea11d20ffdf819f59e516a97abb *man/ligerMethDataset-class.Rd
0f018da2257e4af5f5c00f900d20ed32 *man/ligerRNADataset-class.Rd
5c1b116b853e847fb1b34280a6d92f13 *man/ligerSpatialDataset-class.Rd
ae8c6279cad80a487be10d352be250a9 *man/ligerToSeurat.Rd
7656caea09d8d4a4aeefa7f6578cc38d *man/linkGenesAndPeaks.Rd
cb465ea19abe94f8dd13a08fe8ecc933 *man/louvainCluster-deprecated.Rd
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8e570e396270c154b452da6eda6d75c7 *man/makeInteractTrack-deprecated.Rd
14a83e7eaf446dd69a479764172dba13 *man/makeRiverplot-deprecated.Rd
84cceb1b9900b335d4bfaa43b56bf91b *man/mapCellMeta.Rd
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0f449bba336bea645d8288ac517e944a *man/modalOf.Rd
81d4c821c38871e675c7df1006f5beb1 *man/normalize.Rd
5710da9417b81bca6613c18f4fdbca11 *man/online_iNMF-deprecated.Rd
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438b4f89c05ad42d553f235de3637fd9 *man/optimizeNewData.Rd
a1b0eefd02ec5db8b2e32ea7edefccef *man/optimizeNewK.Rd
c27a223208d5705b8e925ae99213115f *man/optimizeNewLambda.Rd
5f6c83ec737a1923ecbd26e5df7fea4b *man/optimizeSubset.Rd
8073b085531b1fbffc963bae6d93d821 *man/pbmc.Rd
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eec71b3de35642eb45afd8bf26fd764f *man/peak.Rd
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55bfbc4a292807662c6337d86ecf290e *man/plotClusterGeneDot.Rd
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5f8b83ef33083fea153a195e6b0f207e *man/plotDensityDimRed.Rd
9e7cebe1cef93f94ceb1eadb522030ae *man/plotDimRed.Rd
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63c4c67fa0133b8f951445528b46bb3d *man/plotGODot.Rd
caeb8815b8d8d60988552e806b0497f7 *man/plotGeneLoadings.Rd
85da7abbb5e71f6b14db6ee4b8d555f2 *man/plotGroupClusterDimRed.Rd
7a986ccc902ffc0a519747304addbcd5 *man/plotHeatmap.Rd
b312e9b0cf5eeb311cfb879c1a76df07 *man/plotMarkerHeatmap.Rd
206459a66e033da62823a3c69662dc80 *man/plotPairwiseDEGHeatmap.Rd
87911db38bbb30e55529f9fd92fb7c40 *man/plotProportion.Rd
cea5945c3dd08b7c8283b58725561fb1 *man/plotProportionBox.Rd
43c866d723261aaaaf598523565df7f9 *man/plotSankey.Rd
4172cea8217a683a00132cbefcd69165 *man/plotSpatial.Rd
600f9d3d9f82e46a6dd6bcca3732aaf8 *man/plotVarFeatures.Rd
96af38e6398a0c55db8046f766883c13 *man/plotViolin.Rd
8abc45e068d1f7091b00e4ed66c3d158 *man/plotVolcano.Rd
867f7cf6ebca6bca9a536266fb739264 *man/quantileAlignSNF.Rd
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081efbb2c4e636a0b1687d65c5e8e828 *man/read10XFiles.Rd
61a713d9eea349dba911a4b0808ff6c2 *man/readLiger.Rd
4967ee6c17a966e8403f3f30f97c7346 *man/readSubset.Rd
6a483e25e17060e1d6db466d2ed75695 *man/reexports.Rd
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9631988cd33f7a87fa0e6815bcf1bba0 *man/reverseMethData.Rd
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119a1bb65626748f2f226bf64c770a19 *man/runCluster.Rd
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706b4cbbd0f3ec0797a53e112c5e03cf *man/runGOEnrich.Rd
1f1ba80d161c3ccacbecf0309928fadc *man/runGSEA.Rd
530a68c1ce822cf8d30f42d20a88be88 *man/runGeneralQC.Rd
0d65642de20882cc26f83235968bb505 *man/runINMF.Rd
c57ccbc19cc7e2133336ac07c588c546 *man/runIntegration.Rd
7cc35d3f591bb34531ce4bdc25b8d870 *man/runOnlineINMF.Rd
29c784a322ca06797a5597bffdcff61f *man/runTSNE.Rd
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96972a1d035657dfa4d0c1d9e313a07c *man/runUMAP.Rd
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c8a19679681f940226a5c7e3d10ad87e *man/selectGenes.Rd
b71cd3dbcea6b491ab1706425e3b9ce0 *man/selectGenesVST.Rd
b571728a6ec4e46843d0f626d46991ab *man/sub-liger.Rd
b2f67b2047f805e709cd9aea2d1ee73a *man/sub-ligerDataset.Rd
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4d54a4703c8ab522995c19adc7054038 *man/subsetLiger.Rd
00f33b8eff5f0bdf6d3157ef54e19e3a *man/subsetLigerDataset.Rd
ca7abbd5a80129f6ec451e908b563720 *man/updateLigerObject.Rd
22dee0fa1ac0ef518505d73ba73add23 *man/writeH5.Rd
29bfdfcced57d846e658fcb684c0261c *src/Makevars
29bfdfcced57d846e658fcb684c0261c *src/Makevars.win
7e5cf32d81c12a5362b3739355d94802 *src/ModularityOptimizer.cpp
0bfda1b8f1b6d7667f7ef534168b8c8a *src/ModularityOptimizer.h
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5db832d48e966982c47ed3fec34cdcfd *src/centoidAlign.cpp
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fff3def2df358ef7d5f6e32db658eb2b *src/snn.cpp
a28e8648b25d2e780861d74a015e6b32 *src/wilcoxon.cpp
ded24bd60a18e5bbbb6dabea7b75de00 *tests/testthat.R
60bc2815d256b148c687df87569a1247 *tests/testthat/test_downstream.R
f25a8a523edbad3bd641ec84c96e87cd *tests/testthat/test_factorization.R
4106d139fbda6264e3667775fed1ef4d *tests/testthat/test_object.R
22ee8ee44af3e5a73bbbad64185e15f7 *tests/testthat/test_preprocessing.R
ce770ed472038f0c0f3c95dab55d12ed *tests/testthat/test_subset.R
41af3e99cdc651863aa27c6fcd449678 *tests/testthat/test_visualization.R
cb537dd5167779db5505887817f5c076 *vignettes/liger_vignette.Rmd
