235c6df3d6ef52b2a65c7fbb44d2f1d0 *DESCRIPTION
f9766c44344a969ac619cc891ab91fa0 *NAMESPACE
d80ad1c66979df424b7f2acf121d7dd0 *R/RcppExports.R
1a684befd6ec9fef45c8b99694344521 *R/deprecated.R
332b4e63b1b59091187505a9c238563a *R/rliger.R
b8e8f76832afceefa42c967173184eaf *R/utilities.R
c6f805df379cd5f30efeaab78cee3bf3 *README.md
9bc153f1ac120e45fbd86143e330858c *inst/include/rliger.h
b6d29a925440fe3e0985da622234d71a *man/calcARI.Rd
59153c86d35754a4ec2b04e477d6b300 *man/calcAgreement.Rd
23422062a1b1ca43454ffc29315cf475 *man/calcAlignment.Rd
1588204efcc35ee97c131361f87f43d0 *man/calcAlignmentPerCluster.Rd
3b5bba6e7f4a3a6d73cf631eed424690 *man/calcDatasetSpecificity.Rd
34a7802a5039cd04454cf029c050763e *man/calcGeneVars.Rd
c20b3f1f5367e2f946d800fa5a455ad2 *man/calcPurity.Rd
fc4db62475b6468866fbe4ac50b1c98d *man/convertOldLiger.Rd
4be6805c9c54b601f639fc243f927888 *man/createLiger.Rd
3bd9b019c0e7c9c264a5e4e802b6694e *man/getFactorMarkers.Rd
2b806b282a968c72e495afd31c3ece9c *man/getGeneValues.Rd
3844c932f1d7aff3cb273e8a5c268cd4 *man/getProportionMito.Rd
2df4b087a35ff7105e7e01f5d74cf897 *man/imputeKNN.Rd
b5225df3f23c0d19df37740a6c99cc62 *man/liger-class.Rd
98c6d098f1babc4117020728fc6e313e *man/ligerToSeurat.Rd
34e4bab18a5edd23f935c58b4925b52a *man/linkGenesAndPeaks.Rd
f51d3b327f4b813ca31bfd2a828fa42c *man/louvainCluster.Rd
d92afcec885b6810069cd32b9dcc7ec6 *man/makeFeatureMatrix.Rd
72ad2de3113b0c09dd9cd0fdcb90cec0 *man/makeInteractTrack.Rd
a2b6b53cad5f77cebd9fc76a478b5238 *man/makeRiverplot.Rd
374a69a53fd5acb903bfad5b05b7d752 *man/mergeH5.Rd
77758ac9ce1ee126bec14970d2308540 *man/nnzeroGroups.Rd
effd1bded43ae9ba1dff9b200bc309b0 *man/nonneg.Rd
3145aa4d9617b443ea0a7cfbe68cca03 *man/normalize.Rd
12d8a6c949e56b7a42476fe8ce4b900f *man/online_iNMF.Rd
c0c27e7914d06ad0cd0ce7ee6e02a248 *man/optimizeALS.Rd
38415b5cb95ce812cf85241df96ea53c *man/optimizeNewData.Rd
b9f237174021a2344d18a1f1a93307b2 *man/optimizeNewK.Rd
4f202f13a9503110685f15203da832e6 *man/optimizeNewLambda.Rd
6b7503c667b37462b87bef4f68f91d3d *man/optimizeSubset.Rd
4919a8f5a5774fe55159121b29eeeefd *man/plotByDatasetAndCluster.Rd
2194f99b9acfb48a87d0439b360647ac *man/plotClusterFactors.Rd
5489c1baa528bbc335cb1d01a87a32eb *man/plotClusterProportions.Rd
dcbf2a1de07589a4a82e1fd013f4053e *man/plotFactors.Rd
2e41124a7f2d1d6a8d94b29597f10b6c *man/plotFeature.Rd
7e1a2292339e161738ded838fd79d1f2 *man/plotGene.Rd
317b40822685e81f1227ace065ec11a6 *man/plotGeneLoadings.Rd
52be1637afae0267b11eed2745a4a8fa *man/plotGeneViolin.Rd
53c809cfc9589d1e62ccdd8a028451b9 *man/plotGenes.Rd
b8435e47fd8c274dd8bf7a46df515ece *man/plotWordClouds.Rd
ec29a4bcc029526ce0b51ebd084c621d *man/quantileAlignSNF.Rd
ffd18c4b7757bc046e7051683b4ea24a *man/quantile_norm.Rd
2bf863a764165768c4b03ca9e90f7548 *man/rank_matrix.Rd
f25ff06322256af4539a4d9103d3c6fe *man/read10X.Rd
1480d1690b5b391bc2aacea239840539 *man/readSubset.Rd
a0dfcb6018f7ff940ad4831a340b9e6f *man/removeMissingObs.Rd
d951ca0b86dca0ceb287705d1d0dff75 *man/reorganizeLiger.Rd
3116381431a0d32e3888c1d19d0db21d *man/restoreOnlineLiger.Rd
1872b992a65a62f697a365d792b4b743 *man/runGSEA.Rd
4462b4a1e402fb676f7a59bf45d56bfb *man/runTSNE.Rd
a7ba877f88a275b9f21a149782151854 *man/runUMAP.Rd
64a4ea998ea47a677a7a142e6d37b982 *man/runWilcoxon.Rd
44ae22e87cc0cf59c7098c0345cc801f *man/scaleNotCenter.Rd
c7d9205b5a0f0b1f893790c16b01c442 *man/selectGenes.Rd
88c5dacec4d8f4d6453b38b2daae2f95 *man/seuratToLiger.Rd
d1cc14677ad8926fa1508be3a48328f4 *man/show-methods.Rd
d4516703bba86729734643be668c1122 *man/subsetLiger.Rd
914b5ecc55384a848c66ac01ae6d3b5a *man/suggestK.Rd
dd057d87bbd0b6da72cc5351f91c2fd7 *man/suggestLambda.Rd
031315c509dd3d3af3a7b23bdec2a0a0 *man/sumGroups.Rd
22e181e86c8a44467c299691f95aff81 *src/Makevars
7b0aff5765b10fae023b6f2615b28b5e *src/Makevars.win
3e7bc8d512b37a4fbb15aaa05349767f *src/ModularityOptimizer.cpp
4478d72a3694be06ff32fa303ba13852 *src/ModularityOptimizer.h
262eb673da9302200241deb67e40500e *src/RModularityOptimizer.cpp
e6c84e8b53192c59505ebc978c4afcf0 *src/RcppExports.cpp
1e6898c4ba40b1b4e4651d2bb84ce97a *src/data_processing.cpp
9d735dd495bcf7d619b9424325761b40 *src/entities.h
e4d0ab15b0365552fef969c6d4618288 *src/factorization.h
b6f2da687410b46ca45208c9c992f84b *src/fast_wilcox.cpp
a4ad1f9f30cd9303db7d975f10b453a7 *src/feature_mat.cpp
6b932c3e332f876c3da77d53ee095a57 *src/ls.h
dbb5043a12e19c683ebe3ee711836177 *src/mask.h
20ccf9b2a39e4f1eb70b2983995c0b17 *src/matrix.h
ef7b379226b0b1fcc9e65c2408a2e157 *src/nnls.h
077f8122b06ee572933820b9ec9140ce *src/parameters.h
a19b1e6f6a817842c5ca049dd8595155 *src/quantile_norm.cpp
b9762564c79083c41b3f23cba30d39bb *src/run_nmf.cpp
880f8476171cc21ed390beee82e548aa *src/snn.cpp
8bf60682ebafd2bf4bdf94d7640fb7a4 *src/vector.h
c84fb7cdafa84346cbf72b2f4d2be2e3 *tests/testdata/small_pbmc_data.RDS
ded24bd60a18e5bbbb6dabea7b75de00 *tests/testthat.R
b9d97afd9c4c665004bb16edd18d510c *tests/testthat/test_post_factorization.R
0e87ec344baec7e52ae769006ab6bbd9 *tests/testthat/test_preprocessing.R
