Files in yanwu2014/swne
Similarity Weighted Nonnegative Embedding: A method for visualizing high dimensional datasets
.Rbuildignore
.gitignore
DESCRIPTION
Examples/Han_hemato_swne.Rmd
Examples/Han_hemato_swne.html
Examples/cisTopic_quickstart_swne.png
Examples/cortical_neuron_projection.Rmd
Examples/cortical_neuron_projection.html
Examples/hemato_swne.Rmd
Examples/hemato_swne.html
Examples/multiple_pancreas_alignment_swne.Rmd
Examples/multiple_pancreas_alignment_swne.html
Examples/multiple_pancreas_workflow.R
Examples/pbmc3k_swne_matrix.Rmd
Examples/pbmc3k_swne_matrix.html
Examples/pbmc3k_swne_pagoda2.Rmd
Examples/pbmc3k_swne_pagoda2.html
Examples/pbmc3k_swne_seurat.Rmd
Examples/pbmc3k_swne_seurat.html
Examples/scATAC_hemato_swne.Rmd
Examples/scATAC_hemato_swne.html
Examples/seurat_quickstart_swne.png
Examples/zika_swne.Rmd
Examples/zika_swne.html
LICENSE
NAMESPACE
R/RcppExports.R
R/annotate_nmf.R
R/chromatin.R
R/data_processing.R
R/nmf.R
R/paga.R
R/run_swne.R
R/similarity.R
R/swne_plotting.R
README.md
Scripts/Han_hemato_swne.R
Scripts/hemato_swne.R
Scripts/snDropSeq_swne.R
Scripts/splatter_discrete_swne.R
Scripts/splatter_generate.R
Scripts/splatter_helper_functions.R
Scripts/splatter_runtime_analysis.R
Scripts/splatter_trajectory_swne.R
_config.yml
man/AdjustVariance.Rd
man/BuildPAGA.Rd
man/CalcGenesetLoadings.Rd
man/CalcKNN.Rd
man/CalcSNN.Rd
man/CheckGeneEmbedding.Rd
man/ClusterIndicatorMatrix.Rd
man/EmbedFeatures.Rd
man/EmbedPromoters.Rd
man/EmbedSWNE.Rd
man/EmbedTFBS.Rd
man/ExtractField.Rd
man/ExtractNormCounts.Rd
man/ExtractSWNEColors.Rd
man/FactorAssociation.Rd
man/FeaturePlotDims.Rd
man/FeaturePlotSWNE.Rd
man/FilterData.Rd
man/FilterGenesets.Rd
man/FindNumFactors.Rd
man/FlattenGroups.Rd
man/MutualInf.Rd
man/NormalizeCounts.Rd
man/PartitionSimilarityGraph.Rd
man/PlotDims.Rd
man/PlotFactorSelection.Rd
man/PlotSWNE.Rd
man/ProjectFeatures.Rd
man/ProjectGenesets.Rd
man/ProjectSNN.Rd
man/ProjectSWNE.Rd
man/ProjectSamples.Rd
man/PruneSNN.Rd
man/Read10XHuman.Rd
man/ReadData.Rd
man/ReadGenesets.Rd
man/ReadGroups.Rd
man/RenameFactors.Rd
man/RunGSEA.Rd
man/RunNMF.Rd
man/RunSWNE.Rd
man/ScaleCounts.Rd
man/SelectFeatures.Rd
man/SelectGenesets.Rd
man/SummarizeAssocFeatures.Rd
man/UnflattenDataframe.Rd
man/UnflattenGroups.Rd
man/WriteGenesets.Rd
man/WriteGroups.Rd
man/clean_genesets.Rd
man/compute_partitions.Rd
man/compute_projected_snn.Rd
man/ft_transform.Rd
man/genesets_indicator.Rd
man/get_factor_coords.Rd
man/get_sample_coords.Rd
man/ggBarplot.Rd
man/ggHeat.Rd
man/ica_init.Rd
man/kl_div.Rd
man/nnsvd_init.Rd
man/normalize_vector.Rd
man/winsorize_matrix.Rd
src/.gitignore
src/Makevars
src/RcppExports.cpp
src/swne_cpp_funcs.cpp
swne.Rproj
