Files in tinglab/redPATH
Reconstructing the pseudo development time of cell lineages in single cell RNA-Seq data and applications in cancer.
DESCRIPTION
NAMESPACE
R/Evaluation/evaluation_metrics.R
R/HMM code/HMM.R
R/HMM code/baum_welch_code.R
R/HMM code/get_hmm_code.R
R/HMM.R
R/RcppExports.R
R/ai_trial_new.R
R/baum_welch_code.R
R/biological analysis/biological_analysis_plots.R
R/biological analysis/biological_analysis_utils.R
R/biological analysis/g0_identification.R
R/biological_analysis_plots.R
R/biological_analysis_utils.R
R/calc_base_path.R
R/data.R
R/ensemble_path.R
R/evaluation_metrics.R
R/g0_identification.R
R/get_hmm_code.R
R/high_cor_path.R
R/kl_dist_optimized.R
R/preprocess_gene_expression.R
R/redpath_pseudotime.R
README.md
data/GO_differential_genes.RData
data/GO_differential_genes_hs.RData
data/llorens_reCAT_sample_data.RData
data/llorens_sample_data.RData
data/mgh107_sample_data.RData
data/processed_GO.RData
man/bubblesort_index.Rd
man/calc_all_hmm_diff_parallel.Rd
man/calc_correlation.Rd
man/change_index.Rd
man/distribution_plot.Rd
man/ensembl_to_mgi.Rd
man/entrez_to_mgi.Rd
man/filter_exp.Rd
man/gene_selection.Rd
man/gene_selection_intersection.Rd
man/get_GO_exp.Rd
man/get_gene_cluster.Rd
man/get_specific_gene_exprs.Rd
man/hamiltonian_path_as.Rd
man/hamiltonian_path_force.Rd
man/infer_GO_summaries.Rd
man/kendall_correlation.Rd
man/kl_cpp.Rd
man/kmeans_clustering.Rd
man/llorens_exprs.Rd
man/llorens_labels.Rd
man/mean_score_plot.Rd
man/mgh107_portal_exprs.Rd
man/mgh107_portal_labels.Rd
man/mgi_to_entrez.Rd
man/plot_cycle_diff_3d.Rd
man/plot_diff_3d.Rd
man/plot_gene_exprs.Rd
man/plot_heatmap_analysis.Rd
man/plot_hmm_full.Rd
man/plot_specific_gene_exprs.Rd
man/redpath.Rd
man/statistical_test.Rd
redPATH.Rproj
redPATH/DESCRIPTION
redPATH/NAMESPACE
redPATH/R/Evaluation/evaluation_metrics.R
redPATH/R/HMM code/HMM.R
redPATH/R/HMM code/baum_welch_code.R
redPATH/R/HMM code/get_hmm_code.R
redPATH/R/HMM.R
redPATH/R/POS_evaluation.R
redPATH/R/RcppExports.R
redPATH/R/ai_trial.R
redPATH/R/ai_trial_new.R
redPATH/R/baum_welch_code.R
redPATH/R/biological analysis/biological_analysis_plots.R
redPATH/R/biological analysis/biological_analysis_utils.R
redPATH/R/biological analysis/g0_identification.R
redPATH/R/biological_analysis_plots.R
redPATH/R/biological_analysis_utils.R
redPATH/R/calc_base_path.R
redPATH/R/data.R
redPATH/R/ensemble_path.R
redPATH/R/evaluation_metrics.R
redPATH/R/g0_identification.R
redPATH/R/get_hmm_code.R
redPATH/R/high_cor_path.R
redPATH/R/kl_dist_optimized.R
redPATH/R/preprocess_gene_expression.R
redPATH/R/redpath_pseudotime.R
redPATH/README.md
redPATH/data/GO_differential_genes.RData
redPATH/data/GO_differential_genes_hs.RData
redPATH/data/llorens_reCAT_sample_data.RData
redPATH/data/llorens_sample_data.RData
redPATH/data/mgh107_sample_data.RData
redPATH/data/processed_GO.RData
redPATH/man/bubblesort_index.Rd
redPATH/man/calc_all_hmm_diff_parallel.Rd
redPATH/man/calc_correlation.Rd
redPATH/man/change_index.Rd
redPATH/man/distribution_plot.Rd
redPATH/man/ensembl_to_mgi.Rd
redPATH/man/entrez_to_mgi.Rd
redPATH/man/filter_exp.Rd
redPATH/man/gene_selection.Rd
redPATH/man/gene_selection_intersection.Rd
redPATH/man/get_GO_exp.Rd
redPATH/man/get_gene_cluster.Rd
redPATH/man/get_specific_gene_exprs.Rd
redPATH/man/get_start_end.Rd
redPATH/man/hamiltonian_path_ai.Rd
redPATH/man/hamiltonian_path_as.Rd
redPATH/man/hamiltonian_path_force.Rd
redPATH/man/infer_GO_summaries.Rd
redPATH/man/kendall_correlation.Rd
redPATH/man/kl_cpp.Rd
redPATH/man/kmeans_clustering.Rd
redPATH/man/llorens_exprs.Rd
redPATH/man/llorens_labels.Rd
redPATH/man/mean_score_plot.Rd
redPATH/man/mgh107_portal_exprs.Rd
redPATH/man/mgh107_portal_labels.Rd
redPATH/man/mgi_to_entrez.Rd
redPATH/man/plot_cycle_diff_3d.Rd
redPATH/man/plot_diff_3d.Rd
redPATH/man/plot_heatmap_analysis.Rd
redPATH/man/plot_hmm_full.Rd
redPATH/man/plot_specific_gene_exprs.Rd
redPATH/man/pos_score.Rd
redPATH/man/redpath.Rd
redPATH/man/statistical_test.Rd
redPATH/redPATH.Rproj
redPATH/sample_results/overview.jpg
redPATH/sample_results/overview.png
redPATH/src/RcppExports.cpp
redPATH/src/RcppExports.o
redPATH/src/kl_opt.cpp
redPATH/src/kl_opt.o
redPATH/src/matrix_pos.h
redPATH/src/path_insertion_cost.c
redPATH/src/path_insertion_cost.o
redPATH/src/redPATH.dll
sample_results/overview.jpg
sample_results/overview.png
src-i386/RcppExports.cpp
src-i386/RcppExports.o
src-i386/kl_opt.cpp
src-i386/kl_opt.o
src-i386/matrix_pos.h
src-i386/path_insertion_cost.c
src-i386/path_insertion_cost.o
src-i386/redPATH.dll
src-x64/RcppExports.cpp
src-x64/RcppExports.o
src-x64/kl_opt.cpp
src-x64/kl_opt.o
src-x64/matrix_pos.h
src-x64/path_insertion_cost.c
src-x64/path_insertion_cost.o
src-x64/redPATH.dll
src/RcppExports.cpp
src/RcppExports.o
src/kl_opt.cpp
src/kl_opt.o
src/matrix_pos.h
src/path_insertion_cost.c
src/path_insertion_cost.o
src/redPATH.dll
