Files in baumbachlab/keypathwayminer-R
KeyPathwayMiner R-Package
.Rbuildignore
.gitignore
DESCRIPTION
KeyPathwayMineR.Rproj
NAMESPACE
R/all_classes.R
R/kpm.R
R/local.R
R/onLoad.R
R/options.R
R/remote.R
R/utils.R
R/utils_DA.R
R/utils_matrix.R
R/utils_network.R
R/utils_singlecell.R
R/visualization.R
README.md
inst/CITATION
inst/extdata/COAD-VAL-ENTREZ.txt
inst/extdata/datasets/colon-gene-expression-DOWN-p0.05.txt
inst/extdata/datasets/colon-gene-expression-UP-p0.05.txt
inst/extdata/datasets/colon-methylation-matrix-p0.05.txt
inst/extdata/datasets/huntington-gene-expression-DOWN.txt
inst/extdata/datasets/huntington-gene-expression-UP.txt
inst/extdata/datasets_file.txt
inst/extdata/indicator_matrix_hd.txt
inst/extdata/kpm.properties
inst/extdata/negative_list.txt
inst/extdata/positive_list.txt
inst/extdata/sampleNetwork.sif
inst/image/hex/KeyPathwayMineR_hexSticker.png
inst/image/typical_workflow.png
inst/java/keypathwayminer-standalone-5.0.jar
man/Configuration-class.Rd
man/Pathway-class.Rd
man/Result-class.Rd
man/ResultRemote-class.Rd
man/base64EncFile.Rd
man/call_kpm_local.Rd
man/call_kpm_remote.Rd
man/check_files.Rd
man/check_parameters.Rd
man/combine_mutliple_matrices.Rd
man/compute_z_scores.Rd
man/create_indicator_from_fcurdleTest.Rd
man/create_sca.Seurat.Rd
man/create_sca.SingleCellExperiment.Rd
man/create_union_network.Rd
man/dataset_list.Rd
man/determine_union_groups.Rd
man/do_diff_testing_via_MAST.Rd
man/export_graph.Rd
man/export_matrix.Rd
man/export_nodes.Rd
man/export_to_iGraph.Rd
man/fetch_results.Rd
man/filter_fcHurdleTestResults.Rd
man/get_case_exceptions.Rd
man/get_configuration.Rd
man/get_configurations.Rd
man/get_networks.Rd
man/get_pathway.Rd
man/get_pathways.Rd
man/get_result_url.Rd
man/get_results.Rd
man/get_results_from_folder.Rd
man/get_started.Rd
man/get_status.Rd
man/graph_kpm.Rd
man/igraph_to_sif.Rd
man/import_graph.Rd
man/is_finished.Rd
man/kpm.Rd
man/kpm_options.Rd
man/pathway_comparison_plots.Rd
man/pathway_statistics.Rd
man/profile_pathway.Rd
man/quest_progress_url.Rd
man/remove_configuration.Rd
man/reset_options.Rd
man/retrieve_biogrid.Rd
man/save_local_results.Rd
man/save_remote_results.Rd
man/sc_to_indicator_matrix.Rd
man/set_avg_exp.Rd
man/set_num_edges.Rd
man/set_num_nodes.Rd
man/set_pathway.Rd
man/setup_kpm.Rd
man/sif_to_igraph.Rd
man/submit_kpm.Rd
man/test_jvm.Rd
man/to_indicator_matrix.Rd
man/to_java_arguments.Rd
man/visualize_result.Rd
man/withTryCatch.Rd
tests/testthat.R
tests/testthat/test_local.R
tests/testthat/test_remote.R
use_cases/CoV/human_biogrid_network.rds
use_cases/CoV/results_z_1.5.rds
use_cases/CoV/results_z_2.rds
use_cases/CoV/results_z_3.rds
use_cases/CoV/z_score_1_5.rds
use_cases/CoV/z_score_2.rds
use_cases/CoV/z_score_3.rds
use_cases/sars_cov_2.R
use_cases/tabula_muris_senis/LimbMuscleMSC_youngVsOld_ngenes_sex_log2.tsv
use_cases/tabula_muris_senis/LimbMuscleSMSC_youngVsOld_ngenes_sex_log2.tsv
use_cases/tabula_muris_senis/MSC_INESL0T06_K0To10_woBN.rds
use_cases/tabula_muris_senis/SMSC_INESL1T06_K0To10_woBN.rds
use_cases/tabula_muris_senis/analysis_muris_senis.R
use_cases/tabula_muris_senis/filtered_biogrid_mm.sif
vignettes/.gitignore
vignettes/KeyPathwayMineR.Rmd
