Files in NCBI-Hackathons/clustifyR
Classifier for Single-cell RNA-seq Using Cell Clusters
.Rbuildignore
.github/.gitignore
.github/CODE_OF_CONDUCT.md
.github/CONTRIBUTING.md
.github/workflows/check-bioc.yml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/cellbrowsers.R
R/clustifyR-package.R
R/common_dplyr.R
R/compare_genelist.R
R/compute_similarity.R
R/data.R
R/globals.R
R/main.R
R/object_access.R
R/plot.R
R/run_fgsea.R
R/shiny.R
R/utils.R
README.Rmd
README.md
codecov.yml
data-raw/cbmc_m.R
data-raw/cbmc_ref.R
data-raw/downrefs.R
data-raw/hsPBMC_markers.txt
data-raw/human_genes_10x.R
data-raw/mouse_genes_10x.R
data-raw/object_loc_lookup.R
data-raw/pbmc_bulk_matrix.R
data-raw/pbmc_markers.R
data-raw/pbmc_markers_M3Drop.R
data-raw/pbmc_matrix_small.R
data-raw/pbmc_meta.R
data-raw/pbmc_vargenes.R
data/cbmc_m.rda
data/cbmc_ref.rda
data/downrefs.rda
data/human_genes_10x.rda
data/mouse_genes_10x.rda
data/object_loc_lookup.rda
data/pbmc_markers.rda
data/pbmc_markers_M3Drop.rda
data/pbmc_matrix_small.rda
data/pbmc_meta.rda
data/pbmc_vargenes.rda
inst/CITATION
inst/extdata/c2.cp.reactome.v6.2.symbols.gmt.gz
inst/extdata/hsPBMC_markers.txt
inst/scripts/dl_reactome_gene_sets.R
inst/shinyapp/README.md
inst/shinyapp/data/dependencies.csv
inst/shinyapp/data/example-input/get-data.R
inst/shinyapp/data/example-input/matrix.csv.gz
inst/shinyapp/data/example-input/meta-data.csv.gz
inst/shinyapp/global.R
inst/shinyapp/logo.png
inst/shinyapp/server.R
inst/shinyapp/sheet/6c91f3dd95c2217959d38f926b96d7bb_bot4rf@gmail.com
inst/shinyapp/ui.R
inst/shinyapp/www/logo.png
man/append_genes.Rd
man/assess_rank_bias.Rd
man/assign_ident.Rd
man/average_clusters.Rd
man/binarize_expr.Rd
man/build_atlas.Rd
man/calc_distance.Rd
man/calc_similarity.Rd
man/calculate_pathway_gsea.Rd
man/call_consensus.Rd
man/call_to_metadata.Rd
man/cbmc_m.Rd
man/cbmc_ref.Rd
man/check_raw_counts.Rd
man/clustify.Rd
man/clustify_lists.Rd
man/clustify_nudge.Rd
man/clustifyr-package.Rd
man/clustifyr_methods.Rd
man/collapse_to_cluster.Rd
man/compare_lists.Rd
man/cor_to_call.Rd
man/cor_to_call_rank.Rd
man/cor_to_call_topn.Rd
man/cosine.Rd
man/downrefs.Rd
man/downsample_matrix.Rd
man/feature_select_PCA.Rd
man/figures/README-example-1.png
man/figures/README-example-2.png
man/figures/example-1.png
man/figures/example-2.png
man/figures/readme_example-1.png
man/figures/readme_example-2.png
man/figures/test.png
man/file_marker_parse.Rd
man/find_rank_bias.Rd
man/gene_pct.Rd
man/gene_pct_markerm.Rd
man/get_best_match_matrix.Rd
man/get_best_str.Rd
man/get_common_elements.Rd
man/get_similarity.Rd
man/get_ucsc_reference.Rd
man/get_unique_column.Rd
man/get_vargenes.Rd
man/gmt_to_list.Rd
man/human_genes_10x.Rd
man/insert_meta_object.Rd
man/kl_divergence.Rd
man/make_comb_ref.Rd
man/marker_select.Rd
man/matrixize_markers.Rd
man/mouse_genes_10x.Rd
man/not_pretty_palette.Rd
man/object_data.Rd
man/object_loc_lookup.Rd
man/object_ref.Rd
man/overcluster.Rd
man/overcluster_test.Rd
man/parse_loc_object.Rd
man/pbmc_markers.Rd
man/pbmc_markers_M3Drop.Rd
man/pbmc_matrix_small.Rd
man/pbmc_meta.Rd
man/pbmc_vargenes.Rd
man/percent_clusters.Rd
man/permute_similarity.Rd
man/plot_best_call.Rd
man/plot_call.Rd
man/plot_cor.Rd
man/plot_cor_heatmap.Rd
man/plot_dims.Rd
man/plot_gene.Rd
man/plot_pathway_gsea.Rd
man/plot_rank_bias.Rd
man/pos_neg_marker.Rd
man/pos_neg_select.Rd
man/pretty_palette.Rd
man/pretty_palette2.Rd
man/pretty_palette_ramp_d.Rd
man/query_rank_bias.Rd
man/ref_feature_select.Rd
man/ref_marker_select.Rd
man/reverse_marker_matrix.Rd
man/run_clustifyr_app.Rd
man/run_gsea.Rd
man/sce_pbmc.Rd
man/seurat_meta.Rd
man/seurat_ref.Rd
man/so_pbmc.Rd
man/vector_similarity.Rd
man/write_meta.Rd
pkgdown/_pkgdown.yml
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
tests/testthat.R
tests/testthat/.gitignore
tests/testthat/test_cor.R
tests/testthat/test_gsea.R
tests/testthat/test_list.R
tests/testthat/test_plots.R
tests/testthat/test_utils.R
vignettes/.gitignore
vignettes/clustifyr.Rmd
vignettes/geo-annotations.Rmd
