Files in NCBI-Hackathons/clustifyR
Classification of Cell Types in Single-Cell RNA Sequencing Data

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/clustifyR-package.R R/compare_genelist.R R/compute_similarity.R R/data.R R/get_pca_genes.R R/globals.R R/importance_heatmap.R R/main.R R/permutation_similarity.R R/plot.R R/reduce_matrix.R R/refine_clusters.R R/run_fgsea.R R/seurat_wrapper.R R/utils.R README.Rmd README.md
_pkgdown.yml
appveyor.yml
clustifyR.Rproj
codecov.yml
data/pbmc4k_avg.rda
data/pbmc4k_markers.rda
data/pbmc4k_markers_M3Drop.rda
data/pbmc4k_matrix.rda
data/pbmc4k_meta.rda
data/pbmc4k_vargenes.rda
data/pbmc5_markers.rda
data/pbmc5_matrix.rda
data/pbmc5_meta.rda
data/pbmc_bulk_matrix.rda
data/pbmc_pca.rda
docs/CNAME
docs/LICENSE-text.html
docs/articles/clustifyR.html
docs/articles/clustifyR_files/figure-html/plot-1.png
docs/articles/clustifyR_files/figure-html/plot-2.png
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docs/articles/compare_methods.html
docs/articles/exploratory_pca.html
docs/articles/exploratory_pca_files/figure-html/pc_plots-1.png
docs/articles/exploratory_pca_files/figure-html/pc_plots-2.png
docs/articles/exploratory_pca_files/figure-html/pc_plots-3.png
docs/articles/exploratory_pca_files/figure-html/pc_plots-4.png
docs/articles/exploratory_pca_files/figure-html/scree-1.png
docs/articles/gene_list.html
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docs/articles/get_recount_data.html
docs/articles/index.html
docs/articles/random_forest.html
docs/articles/random_forest_files/figure-html/plot-1.png
docs/articles/random_forest_files/figure-html/plot2-1.png
docs/articles/refine_cluster.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/favicon.ico
docs/index.html
docs/inst/images/refine_cluster/initial_random.png
docs/inst/images/refine_cluster/initial_truth.png
docs/inst/images/refine_cluster/iter1.png
docs/inst/images/refine_cluster/iter10.png
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/average_clusters.html
docs/reference/binarize_expr.html
docs/reference/clustify.html
docs/reference/clustifyR.html
docs/reference/clustify_seurat.html
docs/reference/clustifyr_methods.html
docs/reference/compare_lists.html
docs/reference/compute_similarity.html
docs/reference/corr_coef.html
docs/reference/cosine.html
docs/reference/figures/README-example-1.png
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docs/reference/figures/logo.png
docs/reference/figures/logo.svg
docs/reference/getPCAGenes.html
docs/reference/get_best_str.html
docs/reference/get_common_elements.html
docs/reference/get_vargenes.html
docs/reference/importance_heatmap.html
docs/reference/important_heatmap.html
docs/reference/index.html
docs/reference/kl_divergence.html
docs/reference/matrixize_markers.html
docs/reference/pbmc4k_avg.html
docs/reference/pbmc4k_markers.html
docs/reference/pbmc4k_markers_M3Drop.html
docs/reference/pbmc4k_matrix.html
docs/reference/pbmc4k_meta.html
docs/reference/pbmc4k_vargenes.html
docs/reference/pbmc5_markers.html
docs/reference/pbmc5_matrix.html
docs/reference/pbmc5_meta.html
docs/reference/pbmc_bulk_matrix.html
docs/reference/pbmc_pca.html
docs/reference/percent_clusters.html
docs/reference/permutation_similarity.html
docs/reference/plot_call.html
docs/reference/plot_cor.html
docs/reference/plot_gene.html
docs/reference/plot_tsne.html
docs/reference/pretty_palette.html
docs/reference/reduce_expr_matrix.html
docs/reference/refine_clusters.html
docs/reference/run_cor.html
docs/reference/run_gsea.html
docs/reference/select_gene_subset.html
docs/reference/use_seurat_comp.html
docs/reference/vector_similarity.html
docs/sitemap.xml
inst/RForest/random_forest.R inst/RForest/random_forest_write.Rmd inst/RForest/reduce_matrix.R inst/dl_recount.R inst/evaluate_refine_clusters.R
inst/flowchart.png
inst/images/important_predictors.png
inst/images/refine_cluster/initial_random.png
inst/images/refine_cluster/initial_truth.png
inst/images/refine_cluster/iter1.png
inst/images/refine_cluster/iter10.png
inst/images/tsne_plot_PBMC4k.pdf
inst/logo/logo.ai
inst/logo/logo.png
inst/logo/logo_transparent.png
inst/negative_controls.Rmd
inst/note_on_refine_clusters.txt
inst/presentation.pptx
inst/var_genes_M3Drop.Rmd man/average_clusters.Rd man/binarize_expr.Rd man/clustify.Rd man/clustifyR.Rd man/clustifyr_methods.Rd man/compare_lists.Rd man/cosine.Rd
man/figures/README-example-1.png
man/figures/README-example-2.png
man/figures/logo.png
man/figures/logo.svg
man/getPCAGenes.Rd man/get_best_str.Rd man/get_common_elements.Rd man/get_vargenes.Rd man/importance_heatmap.Rd man/kl_divergence.Rd man/matrixize_markers.Rd man/pbmc4k_avg.Rd man/pbmc4k_markers.Rd man/pbmc4k_markers_M3Drop.Rd man/pbmc4k_matrix.Rd man/pbmc4k_meta.Rd man/pbmc4k_vargenes.Rd man/pbmc5_markers.Rd man/pbmc5_matrix.Rd man/pbmc5_meta.Rd man/pbmc_bulk_matrix.Rd man/pbmc_pca.Rd man/percent_clusters.Rd man/plot_call.Rd man/plot_cor.Rd man/plot_gene.Rd man/plot_tsne.Rd man/pretty_palette.Rd man/reduce_expr_matrix.Rd man/refine_clusters.Rd man/run_gsea.Rd man/use_seurat_comp.Rd man/vector_similarity.Rd tests/testthat.R tests/testthat/test_cor.R tests/testthat/test_gsea.R tests/testthat/test_plots.R vignettes/clustifyR.Rmd vignettes/compare_methods.Rmd vignettes/exploratory_pca.Rmd vignettes/gene_list.Rmd vignettes/get_recount_data.Rmd vignettes/random_forest.Rmd vignettes/refine_cluster.Rmd
NCBI-Hackathons/clustifyR documentation built on Sept. 30, 2018, 9:58 a.m.