Files in NCBI-Hackathons/robustSingleCell
Robust Subpopulation dEcision Trees
.Rbuildignore
.gitignore
DESCRIPTION
Dockerfile
LICENSE
NAMESPACE
R/.gitattributes
R/align_functions.R
R/align_functions2.R
R/cost_matrix_functions.R
R/gene_signature.R
R/hierarchy_functions.R
R/preprocess_functions.R
R/test_functions.R
R/tree2_functions.R
R/tree_functions.R
R/visualization.R
README.md
analysis/PhenoGraph_clustering/01_PhenoGraph_clustering.ipynb
analysis/PhenoGraph_clustering/02_jaccard_mapping.ipynb
analysis/PhenoGraph_clustering/03_sensitive_DE.ipynb
analysis/Var_genes.m
analysis/differential_gene_expression/01-define-robust-gene-signature.ipynb
analysis/differential_gene_expression/02-recurse-through-hierarchy.ipynb
analysis/differential_gene_expression/Rscript.R
analysis/differential_gene_expression/correlation_and_jaccard.R
analysis/recurse_tree/t3_DE_recursion.R
data-raw/T3K_T4K_data.R
data-raw/alternative_tree_construction.R
data-raw/generalize_trees.R
data-raw/preprocess-data.R
data-raw/preprocess_CD4_data.R
data-raw/test_configurations.R
data-raw/test_filtering.R
data-raw/tree-matching.R
data/T3K.rda
data/T4K.rda
inst/doc/align_trees.R
inst/doc/align_trees.Rmd
inst/doc/align_trees.html
inst/doc/hierarchy_construction.R
inst/doc/hierarchy_construction.Rmd
inst/doc/hierarchy_construction.html
inst/extdata/3k_pan_T_filtered_gene_bc_matrices/GRCh38/barcodes.tsv
inst/extdata/3k_pan_T_filtered_gene_bc_matrices/GRCh38/genes.tsv
inst/extdata/3k_pan_T_filtered_gene_bc_matrices/GRCh38/matrix.mtx
inst/extdata/3k_pan_T_filtered_gene_bc_matrices/README.txt
inst/extdata/4k_pan_T_filtered_gene_bc_matrices/GRCh38/barcodes.tsv
inst/extdata/4k_pan_T_filtered_gene_bc_matrices/GRCh38/genes.tsv
inst/extdata/4k_pan_T_filtered_gene_bc_matrices/GRCh38/matrix.mtx
inst/extdata/4k_pan_T_filtered_gene_bc_matrices/README.txt
man/DE_level_k.Rd
man/PhenoGraphVarRes.Rd
man/SimpleDE.Rd
man/align.Rd
man/as_binary_tree.Rd
man/as_binary_tree.default.Rd
man/as_binary_tree.hclust.Rd
man/as_binary_tree.phylo.Rd
man/as_phylo.Rd
man/binary_tree.Rd
man/clustertree_construction.Rd
man/construct_hierarchy.Rd
man/cost_matrix.Rd
man/create_align_object.Rd
man/fill_matrix.Rd
man/get_HVG.Rd
man/get_jaccard.Rd
man/initialize.Rd
man/plot.binary_tree.Rd
man/plot.hierarchy.Rd
man/plot_graph.Rd
man/postorder_labels.Rd
man/preprocess_data.Rd
man/sensDE_limma.Rd
man/sens_DE.Rd
man/test_alignment_configuration.Rd
man/test_hierarchy_construction.Rd
man/traceback.Rd
robustSingleCell.Rproj
vignettes/align_trees.Rmd
vignettes/hierarchy_construction.Rmd
