base64EncFile | Method for base64 encoding |
call_kpm_local | Method for running KeyPathwayMineR localy |
call_kpm_remote | Method for running KeyPathwayMineR remotely |
check_files | Function which checks and processes files |
check_parameters | Function which check parameters |
combine_mutliple_matrices | Logically combines multiple datasets |
compute_z_scores | Computes z-score values of case samples |
Configuration-class | A configuration of the parameters K and L |
create_indicator_from_fcurdleTest | Creates indicator matrix from differentail |
create_sca.Seurat | Converts Seurat object to SingleCellAssay object |
create_sca.SingleCellExperiment | Converts SingleCellExperiment object to SingleCellAssay... |
create_union_network | Creates a union network for the pathways of a specific... |
dataset_list | Encodes a list of datasets |
determine_union_groups | Determines from which pathways a node originates |
do_diff_testing_via_MAST | Calculates differentially expressed genes from single cell... |
export_graph | Export a graph |
export_matrix | Saves indicator matrix as a file. |
export_nodes | Export node ids |
export_to_iGraph | Get an iGraph object for a specific pathway |
fetch_results | Once the run is complete, we can obtain the results |
filter_fcHurdleTestResults | Filters the differential expression analysis results based on... |
get_case_exceptions | Creates java arguments for case exceptions |
get_configuration | Get configuration object |
get_configurations | Get all configuration names of a result |
get_networks | Get a data frame of available networks |
get_pathway | Get specific pathway of a configuration |
get_pathways | Get all pathways for a specific configuration |
get_results | Fetches result for remote run. |
get_results_from_folder | Loads results from folder with text files |
get_result_url | Returns result url |
get_started | Functions which prints information on how to get started. |
get_status | Method to check up on a submitted job. |
graph_kpm | Helper method to encode custom network file |
igraph_to_sif | Converts igraph object to sif file. |
import_graph | Reads graph file and converts it to igraph object |
is_finished | Check if asynchronous remote run is finished |
kpm | Main method used for running KPM |
kpm_options | Set or get options for KeyPathwayMineR |
Pathway-class | A pathway of a specific configuration. |
pathway_comparison_plots | Two pathway comparison plots. |
pathway_statistics | Computes pathway statistics for all pathways in a result... |
profile_pathway | Run gprofiler2's gost function on pathway of interesst |
quest_progress_url | Get progress url |
remove_configuration | Removes configuration from result object |
reset_options | Resets kpm_options to default values |
Result-class | Result |
ResultRemote-class | ResultRemote |
retrieve_biogrid | Retrieves bioGRID network in suitable form for KPM |
save_local_results | Save results of the local run |
save_remote_results | Save results of the remote run |
sc_to_indicator_matrix | Calculates differentially expressed genes from single cell... |
set_avg_exp | Set average differential expressed cases per gene |
set_num_edges | Set number of edges given pathway object |
set_num_nodes | Set number of nodes given pathway object |
set_pathway | Set pathway |
setup_kpm | Set up a JSON object in preparation of the job submission |
sif_to_igraph | Convert sif file to iGraph object |
submit_kpm | Method for submitting a job to KeyPathwayMinerWeb Submits can... |
test_jvm | Checks the version of the JVM. |
to_indicator_matrix | Convertes numerical matrix to an indicator matrix |
to_java_arguments | Method which transform kpm_options() to java arguments. |
visualize_result | Shiny App for KeyPathwayMineR results |
withTryCatch | Helper method for error handling |
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