.Rbuildignore
.gitignore
CITATION.cff
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/data.R
R/evaluation.R
R/finalClustering.R
R/getDistMat.R
R/getIDER.R
R/initialClustering.R
R/mergeInitialClusters.R
R/plotDistMat.R
R/plotNetwork.R
R/scatterPlot.R
R/utils.R
README.Rmd
README.md
_pkgdown.yml
data/dendritic.rda
data/pancreas.RData
data/pancreas_counts.RData
data/pancreas_meta.RData
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/asCIDER.html
docs/articles/asCIDER_files/figure-html/heatmap-1.png
docs/articles/asCIDER_files/figure-html/scatterPlot-confounded-1.png
docs/articles/asCIDER_files/figure-html/summary-tsne-plots-1.png
docs/articles/asCIDER_files/figure-html/unnamed-chunk-3-1.png
docs/articles/asCIDER_files/figure-html/unnamed-chunk-4-1.png
docs/articles/asCIDER_files/figure-html/unnamed-chunk-5-1.png
docs/articles/asCIDER_files/figure-html/unnamed-chunk-6-1.png
docs/articles/asCIDER_files/header-attrs-2.11/header-attrs.js
docs/articles/dnCIDER.html
docs/articles/dnCIDER_files/figure-html/plot-network-1.png
docs/articles/dnCIDER_files/figure-html/tsne-plot-CIDER-results-1.png
docs/articles/dnCIDER_files/figure-html/unnamed-chunk-10-1.png
docs/articles/dnCIDER_files/figure-html/unnamed-chunk-11-1.png
docs/articles/dnCIDER_files/figure-html/unnamed-chunk-12-1.png
docs/articles/dnCIDER_files/figure-html/unnamed-chunk-5-1.png
docs/articles/dnCIDER_files/figure-html/unnamed-chunk-7-1.png
docs/articles/dnCIDER_files/figure-html/unnamed-chunk-7-2.png
docs/articles/dnCIDER_files/header-attrs-2.11/header-attrs.js
docs/articles/dnCIDER_highlevel.html
docs/articles/dnCIDER_highlevel_files/figure-html/tsne-plot-CIDER-results-1.png
docs/articles/dnCIDER_highlevel_files/figure-html/tsne-plot-ground-truth-1.png
docs/articles/dnCIDER_highlevel_files/header-attrs-2.11/header-attrs.js
docs/articles/evaluation.html
docs/articles/evaluation_files/figure-html/unnamed-chunk-10-1.png
docs/articles/evaluation_files/figure-html/unnamed-chunk-6-1.png
docs/articles/evaluation_files/figure-html/unnamed-chunk-7-1.png
docs/articles/evaluation_files/figure-html/unnamed-chunk-8-1.png
docs/articles/evaluation_files/figure-html/unnamed-chunk-9-1.png
docs/articles/evaluation_files/header-attrs-2.11/header-attrs.js
docs/articles/evaluation_obsolete.html
docs/articles/evaluation_obsolete_files/header-attrs-2.11/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js
docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.1.0/bootstrap.min.css
docs/deps/bootstrap-5.1.0/font.css
docs/deps/bootstrap-5.1.0/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVs9pbCIPrc.woff
docs/deps/bootstrap-5.1.0/fonts/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrc.woff
docs/deps/bootstrap-5.1.0/fonts/4iCs6KVjbNBYlgo6ew.woff
docs/deps/bootstrap-5.1.0/fonts/4iCs6KVjbNBYlgoKfw7w.woff
docs/deps/bootstrap-5.1.0/fonts/4iCv6KVjbNBYlgoCxCvTtA.woff
docs/deps/bootstrap-5.1.0/fonts/4iCv6KVjbNBYlgoCxCvjsGyL.woff
docs/deps/bootstrap-5.1.0/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPZ7nsDQ.woff
docs/deps/bootstrap-5.1.0/fonts/6xK1dSBYKcSV-LCoeQqfX1RYOo3qPa7j.woff
docs/deps/bootstrap-5.1.0/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3aPA.woff
docs/deps/bootstrap-5.1.0/fonts/6xK3dSBYKcSV-LCoeQqfX1RYOo3qOK7j.woff
docs/deps/bootstrap-5.1.0/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3i54rAkw.woff
docs/deps/bootstrap-5.1.0/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vAkw.woff
docs/deps/bootstrap-5.1.0/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ig4vwlxdo.woff
docs/deps/bootstrap-5.1.0/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zAkw.woff
docs/deps/bootstrap-5.1.0/fonts/6xKydSBYKcSV-LCoeQqfX1RYOo3ik4zwlxdo.woff
docs/deps/bootstrap-5.1.0/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvWNRevw.woff
docs/deps/bootstrap-5.1.0/fonts/CSR54z1Qlv-GDxkbKVQ_dFsvaNA.woff
docs/deps/bootstrap-5.1.0/fonts/CSR64z1Qlv-GDxkbKVQ_TOQ.woff
docs/deps/bootstrap-5.1.0/fonts/CSR64z1Qlv-GDxkbKVQ_fOAKSw.woff
docs/deps/bootstrap-5.1.0/fonts/JTURjIg1_i6t8kCHKm45_ZpC7g0.woff
docs/deps/bootstrap-5.1.0/fonts/JTURjIg1_i6t8kCHKm45_dJE7g0.woff
docs/deps/bootstrap-5.1.0/fonts/JTUSjIg1_i6t8kCHKm45xW0.woff
docs/deps/bootstrap-5.1.0/fonts/KFOlCnqEu92Fr1MmEU9fBBc-.woff
docs/deps/bootstrap-5.1.0/fonts/KFOlCnqEu92Fr1MmEU9vAA.woff
docs/deps/bootstrap-5.1.0/fonts/KFOlCnqEu92Fr1MmSU5fBBc-.woff
docs/deps/bootstrap-5.1.0/fonts/KFOlCnqEu92Fr1MmSU5vAA.woff
docs/deps/bootstrap-5.1.0/fonts/KFOlCnqEu92Fr1MmWUlfBBc-.woff
docs/deps/bootstrap-5.1.0/fonts/KFOlCnqEu92Fr1MmWUlvAA.woff
docs/deps/bootstrap-5.1.0/fonts/KFOmCnqEu92Fr1Me5g.woff
docs/deps/bootstrap-5.1.0/fonts/KFOmCnqEu92Fr1Mu4mxM.woff
docs/deps/bootstrap-5.1.0/fonts/QGYpz_kZZAGCONcK2A4bGOj8mNhL.woff
docs/deps/bootstrap-5.1.0/fonts/S6u8w4BMUTPHjxsAXC-s.woff
docs/deps/bootstrap-5.1.0/fonts/S6u8w4BMUTPHjxswWA.woff
docs/deps/bootstrap-5.1.0/fonts/S6u9w4BMUTPHh6UVSwiPHw.woff
docs/deps/bootstrap-5.1.0/fonts/S6u9w4BMUTPHh6UVeww.woff
docs/deps/bootstrap-5.1.0/fonts/S6u9w4BMUTPHh7USSwiPHw.woff
docs/deps/bootstrap-5.1.0/fonts/S6u9w4BMUTPHh7USeww.woff
docs/deps/bootstrap-5.1.0/fonts/S6uyw4BMUTPHjx4wWA.woff
docs/deps/bootstrap-5.1.0/fonts/S6uyw4BMUTPHvxo.woff
docs/deps/bootstrap-5.1.0/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuFuYMZs.woff
docs/deps/bootstrap-5.1.0/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuI6fMZs.woff
docs/deps/bootstrap-5.1.0/fonts/UcCO3FwrK3iLTeHuS_fvQtMwCp50KnMw2boKoduKmMEVuLyfMZs.woff
docs/deps/bootstrap-5.1.0/fonts/XRXV3I6Li01BKof4MQ.woff
docs/deps/bootstrap-5.1.0/fonts/XRXW3I6Li01BKofA6sKkZQ.woff
docs/deps/bootstrap-5.1.0/fonts/XRXW3I6Li01BKofAjsOkZQ.woff
docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkWVAexg.woff
docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk5hkaVQ.woff
docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkWVAexg.woff
docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0Rk8ZkaVQ.woff
docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjWVAexg.woff
docs/deps/bootstrap-5.1.0/fonts/memQYaGs126MiZpBA-UFUIcVXSCEkx2cmqvXlWq8tWZ0Pw86hd0RkyFjaVQ.woff
docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1x4gaVQ.woff
docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsg-1y4k.woff
docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0B4gaVQ.woff
docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsiH0C4k.woff
docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0B4gaVQ.woff
docs/deps/bootstrap-5.1.0/fonts/memSYaGs126MiZpBA-UvWbX2vVnXBbObj2OVZyOOSr4dVJWUgsjZ0C4k.woff
docs/deps/bootstrap-5.1.0/fonts/pe03MImSLYBIv1o4X1M8cc9iB_5p.woff
docs/deps/bootstrap-5.1.0/fonts/pe0qMImSLYBIv1o4X1M8cfe5.woff
docs/deps/bootstrap-5.1.0/fonts/q5uGsou0JOdh94bfvQlr.woff
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CIDEr-package.html
docs/reference/Merge.html
docs/reference/Rplot001.png
docs/reference/calculateDistMatOneModel.html
docs/reference/cosineSimilarityR.html
docs/reference/cosine_similarity.html
docs/reference/dendritic.html
docs/reference/downsampling.html
docs/reference/estimateProb.html
docs/reference/figures/README-pressure-1.png
docs/reference/figures/card.png
docs/reference/figures/clustering_diagram.png
docs/reference/figures/evaluation_scatterplot.png
docs/reference/figures/logo.png
docs/reference/finalClustering.html
docs/reference/gatherInitialClusters.html
docs/reference/getDistMat.html
docs/reference/getGroupFit.html
docs/reference/getIDEr.html
docs/reference/hdbscan.seurat.html
docs/reference/index.html
docs/reference/initialClustering.html
docs/reference/measureSimilarity.html
docs/reference/mergeInitialClusters.html
docs/reference/pancreas.html
docs/reference/pancreas_counts.html
docs/reference/pancreas_meta.html
docs/reference/plotDistMat.html
docs/reference/plotHeatmap.html
docs/reference/plotNetwork.html
docs/reference/rcpp_hello_world.html
docs/reference/scatterPlot-1.png
docs/reference/scatterPlot.html
docs/search.json
docs/sitemap.xml
man/Merge.Rd
man/calculateDistMatOneModel.Rd
man/cosineSimilarityR.Rd
man/downsampling.Rd
man/estimateProb.Rd
man/figures/card.png
man/figures/clustering_diagram.png
man/figures/evaluation_scatterplot.png
man/figures/logo.png
man/finalClustering.Rd
man/getDistMat.Rd
man/getGroupFit.Rd
man/getIDEr.Rd
man/hdbscan.seurat.Rd
man/initialClustering.Rd
man/measureSimilarity.Rd
man/mergeInitialClusters.Rd
man/pancreas.Rd
man/plotDistMat.Rd
man/plotHeatmap.Rd
man/plotNetwork.Rd
man/scatterPlot.Rd
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
vignettes/asCIDER.Rmd
vignettes/asCIDER.html
vignettes/dnCIDER.Rmd
vignettes/dnCIDER.html
vignettes/dnCIDER_highlevel.Rmd
vignettes/dnCIDER_highlevel.html
vignettes/evaluation.Rmd
vignettes/evaluation.html