Files in stemangiola/ARMET
Higher-Order Deconvolution Survival Analyses
.Rbuildignore
.gitattributes
.github/.gitignore
.github/workflows/check-bioc.yml
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
R/ARMET-package.R
R/data.R
R/functions_NON_hierarchical.R
R/functions_hierarchical.R
R/methods.R
R/nanny_methods.R
R/plotting.R
R/stanmodels.R
R/utility.R
R/validation.R
README.Rmd
README.md
configure
data/ancestor_child.rda
data/cmdstanr_ARMET_tc_fix_hierarchical.rda
data/ct_names_polar.rda
data/hierarchy_reference.rda
data/house_keeping_genes.rda
data/n_markers.rda
data/no_hierarchy_reference.rda
data/test_mixture.rda
data/tree.rda
dev/HPC_run_ARMET_on_TCGA.sh
dev/TCGA_survival_cibersort.R
dev/censoring.R
dev/comparison_NB_waring.R
dev/create_mix_dirichlet.R
dev/create_mix_noisless_studentt.R
dev/create_mix_source.R
dev/figures_TCGA.R
dev/hk_600.txt
dev/hmap_association.pdf
dev/hmap_composition.pdf
dev/jacobian.R
dev/job_step_1_ref_building.sh
dev/makefile_run_ARMET_on_TCGA
dev/makefile_run_ARMET_on_TCGA_gender
dev/proof_of_concept.R
dev/run_armet_on_cancer_type.R
dev/run_armet_on_cancer_type.sh
dev/simulation_benchmark.png
dev/step_0_ref_building.R
dev/step_1_ref_building.R
dev/step_2_ref_building.R
dev/step_3_ref_building.R
dev/sum_proportion_NB.R
dev/survival_modeling_TCGA.R
dev/tanglegram.pdf
dev/test_simulation_makeflow_pipeline/asses_accuracy.R
dev/test_simulation_makeflow_pipeline/create_input.R
dev/test_simulation_makeflow_pipeline/create_makefile.R
dev/test_simulation_makeflow_pipeline/infer.R
dev/test_simulation_makeflow_pipeline/makefile_test_simulation.makeflow
dev/test_simulation_makeflow_pipeline/test_simulation_survival.R
dev/test_simulation_makeflow_pipeline/third_party_reference.rds
dev/test_simulation_singleCell_makeflow_pipeline/asses_accuracy.R
dev/test_simulation_singleCell_makeflow_pipeline/create_input.R
dev/test_simulation_singleCell_makeflow_pipeline/create_makefile.R
dev/test_simulation_singleCell_makeflow_pipeline/infer.R
dev/test_simulation_singleCell_makeflow_pipeline/makefile_test_simulation.makeflow
dev/test_simulation_singleCell_makeflow_pipeline/parse_benign.R
dev/test_simulation_singleCell_makeflow_pipeline/test_simulation_survival.R
dev/validation_CyTOF.R
dev/validation_single_cell.R
inst/extdata/tree.yaml
inst/include/armet_logo.png
inst/include/armet_polar.png
inst/include/stan_meta_header.hpp
inst/stan/ARMET_tc_fix.stan
inst/stan/ARMET_tc_fix_hierarchical.stan
inst/stan/censored_regression.stan
inst/stan/generated_quantities.stan
inst/stan/generated_quantities_lv1.stan
inst/stan/generated_quantities_lv2.stan
inst/stan/generated_quantities_lv3.stan
inst/stan/generated_quantities_lv4.stan
inst/stan/include/license.stan
man/ARMET-package.Rd
man/ARMET_tc_continue.Rd
man/add_cox_test.Rd
man/ancestor_child.Rd
man/as_matrix.Rd
man/cmdstanr_ARMET_tc_fix_hierarchical.Rd
man/convoluted_glm.Rd
man/create_design_matrix.Rd
man/ct_names_polar.Rd
man/error_if_counts_is_na.Rd
man/error_if_duplicated_genes.Rd
man/estimate_convoluted_lm.Rd
man/get_sample_transcript_counts.Rd
man/hierarchy_reference.Rd
man/house_keeping_genes.Rd
man/ifelse2_pipe.Rd
man/ifelse3_pipe.Rd
man/ifelse4_pipe.Rd
man/ifelse_pipe.Rd
man/n_markers.Rd
man/no_hierarchy_reference.Rd
man/plot_markers.Rd
man/plot_polar.Rd
man/plot_scatter.Rd
man/setup_convolved_lm.Rd
man/tree.Rd
man/vb_iterative.Rd
src/ARMET.so.REMOVED.git-id
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/stanExports_ARMET_tc.cc
src/stanExports_ARMET_tc.h
tests/testthat.R
tests/testthat/tests.R
