Files in kharchenkolab/conos
Clustering on Network of Samples
.Rbuildignore
.Rinstignore
.circleci/config.yml
.gitattributes
.gitignore
CHANGELOG.md
CONTRIBUTING.md
DESCRIPTION
LICENSE.md
NAMESPACE
R/RcppExports.R
R/access_wrappers.R
R/communities.R
R/conclass.R
R/conos.R
R/data.R
R/de_functions.R
R/graph_embedding.R
R/integrations.R
R/largeVis.R
R/plot.R
README.md
conos.Rproj
data-raw/create_rdata_file.R
data/small_panel.preprocessed.rda
doc/adjust_alignment_strength.R
doc/adjust_alignment_strength.Rmd
doc/adjust_alignment_strength.html
doc/adjust_alignment_strength.md
doc/figure_adjust_alignment_strength/unnamed-chunk-10-1.png
doc/figure_adjust_alignment_strength/unnamed-chunk-12-1.png
doc/figure_adjust_alignment_strength/unnamed-chunk-14-1.png
doc/figure_adjust_alignment_strength/unnamed-chunk-16-1.png
doc/figure_adjust_alignment_strength/unnamed-chunk-5-1.png
doc/figure_adjust_alignment_strength/unnamed-chunk-5-2.png
doc/figure_adjust_alignment_strength/unnamed-chunk-6-1.png
doc/figure_adjust_alignment_strength/unnamed-chunk-8-1.png
doc/figure_integrating_rnaseq_atacseq/unnamed-chunk-7-1.png
doc/figure_walkthrough/unnamed-chunk-12-1.png
doc/figure_walkthrough/unnamed-chunk-13-1.png
doc/figure_walkthrough/unnamed-chunk-15-1.png
doc/figure_walkthrough/unnamed-chunk-16-1.png
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doc/figure_walkthrough/unnamed-chunk-44-1.png
doc/figure_walkthrough/unnamed-chunk-45-1.png
doc/figure_walkthrough/unnamed-chunk-46-1.png
doc/figure_walkthrough/unnamed-chunk-47-1.png
doc/figure_walkthrough/unnamed-chunk-54-1.png
doc/figure_walkthrough/unnamed-chunk-55-1.png
doc/integrating_rnaseq_atacseq.R
doc/integrating_rnaseq_atacseq.Rmd
doc/integrating_rnaseq_atacseq.html
doc/integrating_rnaseq_atacseq.md
doc/scanpy_integration.R
doc/scanpy_integration.Rmd
doc/scanpy_integration.html
doc/scanpy_integration.md
doc/walkthrough.R
doc/walkthrough.Rmd
doc/walkthrough.html
doc/walkthrough.md
docker/Dockerfile
inst/COPYRIGHTS
inst/conos_logo.png
inst/extdata/cellannot.txt
inst/scanpy_integration.ipynb
man/Conos.Rd
man/armaCor.Rd
man/basicSeuratProc.Rd
man/bestClusterThresholds.Rd
man/bestClusterTreeThresholds.Rd
man/buildWijMatrix.Rd
man/checkCountsWholeNumbers.Rd
man/convertToPagoda2.Rd
man/edgeMat.Rd
man/estimateWeightEntropyPerCell.Rd
man/filter.genes.by.cluster.expression.Rd
man/findSubcommunities.Rd
man/getBetweenCellTypeCorrectedDE.Rd
man/getBetweenCellTypeDE.Rd
man/getCellNames.Rd
man/getClusterRelationshipConsistency.Rd
man/getClustering.Rd
man/getClusteringGroups.Rd
man/getCountMatrix.Rd
man/getEmbedding.Rd
man/getGeneExpression.Rd
man/getGenes.Rd
man/getGlobalClusterMarkers.Rd
man/getNeighborMatrix.Rd
man/getOdGenesUniformly.Rd
man/getOverdispersedGenes.Rd
man/getPca.Rd
man/getPerCellTypeDE.Rd
man/getPercentGlobalClusters.Rd
man/getRawCountMatrix.Rd
man/getSampleNamePerCell.Rd
man/greedyModularityCut.Rd
man/multimulti.community.Rd
man/multitrap.community.Rd
man/namedLevels.Rd
man/namedNames.Rd
man/p2app4conos.Rd
man/plotClusterBarplots.Rd
man/plotClusterBoxPlotsByAppType.Rd
man/plotComponentVariance.Rd
man/plotDEheatmap.Rd
man/plotEmbeddings.Rd
man/plotSamples.Rd
man/projectKNNs.Rd
man/propagateLabelsDiffusion.Rd
man/quickCCA.Rd
man/quickCPCA.Rd
man/quickPlainPCA.Rd
man/rawMatricesWithCommonGenes.Rd
man/reexports.Rd
man/saveConosForScanPy.Rd
man/saveDEasCSV.Rd
man/saveDEasJSON.Rd
man/scanKModularity.Rd
man/sgdBatches.Rd
man/small_panel.preprocessed.Rd
man/stableTreeClusters.Rd
man/velocityInfoConos.Rd
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/Rjnmf.cpp
src/adjustedRand.cpp
src/checkfunctions.cpp
src/cpca.cpp
src/deltacut.cpp
src/edgeFilter.cpp
src/edge_rebalancing.cpp
src/edgeweights.cpp
src/gradients.cpp
src/graph_embedding.cpp
src/include/alias.h
src/include/gradients.h
src/include/largeVis.h
src/largeVis.cpp
src/propagate_labels.cpp
src/spcov.cpp
tests/testthat.R
tests/testthat/test_functions.R
