# Cytobank API Wrapper for R

## Documentation for package ‘CytobankAPI’ version 2.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H N O P S T U V

## -- A --

AdvancedAnalysis-class | S4 Advanced Analysis Class
attachments | Attachment Endpoints
attachments.delete | Attachment Endpoints
attachments.delete-method | Attachment Endpoints
attachments.download | Attachment Endpoints
attachments.download-method | Attachment Endpoints
attachments.download_zip | Attachment Endpoints
attachments.download_zip-method | Attachment Endpoints
attachments.list | Attachment Endpoints
attachments.list-method | Attachment Endpoints
attachments.show | Attachment Endpoints
attachments.show-method | Attachment Endpoints
attachments.update | Attachment Endpoints
attachments.update-method | Attachment Endpoints
attachments.upload | Attachment Endpoints
attachments.upload-method | Attachment Endpoints
authenticate | Authentication Endpoints
authentication | Authentication Endpoints
authentication.logout | Authentication Endpoints
authentication.logout-method | Authentication Endpoints
authentication.revoke_all_tokens | Authentication Endpoints
authentication.revoke_all_tokens-method | Authentication Endpoints
authentication.revoke_all_tokens_user | Authentication Endpoints
authentication.revoke_all_tokens_user-method | Authentication Endpoints
autogating | Automatic gating Endpoints
autogating.copy_autogating_analysis_settings | Automatic gating Endpoints
autogating.copy_autogating_analysis_settings-method | Automatic gating Endpoints
autogating.create_autogating_analysis | Automatic gating Endpoints
autogating.create_autogating_analysis-method | Automatic gating Endpoints
autogating.delete_autogating_analysis | Automatic gating Endpoints
autogating.delete_autogating_analysis-method | Automatic gating Endpoints
autogating.list_autogating_analyses_of_type | Automatic gating Endpoints
autogating.list_autogating_analyses_of_type-method | Automatic gating Endpoints
autogating.rename_autogating_analysis | Automatic gating Endpoints
autogating.rename_autogating_analysis-method | Automatic gating Endpoints
autogating.run_autogating_analysis | Automatic gating Endpoints
autogating.run_autogating_analysis-method | Automatic gating Endpoints
autogating.show_autogating_analysis_details | Automatic gating Endpoints
autogating.show_autogating_analysis_details-method | Automatic gating Endpoints
autogating.show_autogating_analysis_status | Automatic gating Endpoints
autogating.show_autogating_analysis_status-method | Automatic gating Endpoints
autogating.update_autogating_inference_analysis_details | Automatic gating Endpoints
autogating.update_autogating_inference_analysis_details-method | Automatic gating Endpoints
autogating.update_autogating_training_analysis_details | Automatic gating Endpoints
autogating.update_autogating_training_analysis_details-method | Automatic gating Endpoints

## -- C --

citrus | CITRUS Endpoints
CITRUS-class | S4 CITRUS Class
citrus.copy_settings | CITRUS Endpoints
citrus.copy_settings-method | CITRUS Endpoints
citrus.delete | CITRUS Endpoints
citrus.delete-method | CITRUS Endpoints
citrus.download | CITRUS Endpoints
citrus.download-method | CITRUS Endpoints
citrus.list | CITRUS Endpoints
citrus.list-method | CITRUS Endpoints
citrus.new | CITRUS Endpoints
citrus.new-method | CITRUS Endpoints
citrus.rename | CITRUS Endpoints
citrus.rename-method | CITRUS Endpoints
citrus.run | CITRUS Endpoints
citrus.run-method | CITRUS Endpoints
citrus.show | CITRUS Endpoints
citrus.show-method | CITRUS Endpoints
citrus.status | CITRUS Endpoints
citrus.status-method | CITRUS Endpoints
citrus.update | CITRUS Endpoints
citrus.update-method | CITRUS Endpoints
compensations | Compensation Endpoints
compensations.list | Compensation Endpoints
compensations.list-method | Compensation Endpoints
compensations.show | Compensation Endpoints
compensations.show-method | Compensation Endpoints
compensations.upload_csv | Compensation Endpoints
compensations.upload_csv-method | Compensation Endpoints
CytobankAPI_news | News

## -- D --

DimensionalityReduction-class | S4 DimensionalityReduction Class
dimensionality_reduction | DimensionalityReduction Endpoints
dimensionality_reduction.copy_settings | DimensionalityReduction Endpoints
dimensionality_reduction.copy_settings-method | DimensionalityReduction Endpoints
dimensionality_reduction.delete | DimensionalityReduction Endpoints
dimensionality_reduction.delete-method | DimensionalityReduction Endpoints
dimensionality_reduction.list | DimensionalityReduction Endpoints
dimensionality_reduction.list-method | DimensionalityReduction Endpoints
dimensionality_reduction.new | DimensionalityReduction Endpoints
dimensionality_reduction.new-method | DimensionalityReduction Endpoints
dimensionality_reduction.rename | DimensionalityReduction Endpoints
dimensionality_reduction.rename-method | DimensionalityReduction Endpoints
dimensionality_reduction.run | DimensionalityReduction Endpoints
dimensionality_reduction.run-method | DimensionalityReduction Endpoints
dimensionality_reduction.show | DimensionalityReduction Endpoints
dimensionality_reduction.show-method | DimensionalityReduction Endpoints
dimensionality_reduction.status | DimensionalityReduction Endpoints
dimensionality_reduction.status-method | DimensionalityReduction Endpoints
dimensionality_reduction.update | DimensionalityReduction Endpoints
dimensionality_reduction.update-method | DimensionalityReduction Endpoints
drop | DROP File Endpoints
drop.upload | DROP File Endpoints
drop.upload-method | DROP File Endpoints

## -- E --

experiments | Experiment Endpoints
experiments.clone_full | Experiment Endpoints
experiments.clone_full-method | Experiment Endpoints
experiments.clone_selective | Experiment Endpoints
experiments.clone_selective-method | Experiment Endpoints
experiments.delete | Experiment Endpoints
experiments.delete-method | Experiment Endpoints
experiments.full_access_users_add | Experiment Endpoints
experiments.full_access_users_add-method | Experiment Endpoints
experiments.full_access_users_list | Experiment Endpoints
experiments.full_access_users_list-method | Experiment Endpoints
experiments.full_access_users_remove | Experiment Endpoints
experiments.full_access_users_remove-method | Experiment Endpoints
experiments.list | Experiment Endpoints
experiments.list-method | Experiment Endpoints
experiments.new | Experiment Endpoints
experiments.new-method | Experiment Endpoints
experiments.show | Experiment Endpoints
experiments.show-method | Experiment Endpoints
experiments.trash | Experiment Endpoints
experiments.trash-method | Experiment Endpoints
experiments.update | Experiment Endpoints
experiments.update-method | Experiment Endpoints

## -- F --

fcs_files | FCS File Endpoints
fcs_files.download | FCS File Endpoints
fcs_files.download-method | FCS File Endpoints
fcs_files.download_zip | FCS File Endpoints
fcs_files.download_zip-method | FCS File Endpoints
fcs_files.file_internal_comp_show | FCS File Endpoints
fcs_files.file_internal_comp_show-method | FCS File Endpoints
fcs_files.list | FCS File Endpoints
fcs_files.list-method | FCS File Endpoints
fcs_files.show | FCS File Endpoints
fcs_files.show-method | FCS File Endpoints
fcs_files.status | FCS File Endpoints
fcs_files.status-method | FCS File Endpoints
fcs_files.upload | FCS File Endpoints
fcs_files.upload-method | FCS File Endpoints
fcs_files.upload_zip | FCS File Endpoints
fcs_files.upload_zip-method | FCS File Endpoints
flowsom | FlowSOM Endpoints
FlowSOM-class | S4 FlowSOM Class
flowsom.copy_settings | FlowSOM Endpoints
flowsom.copy_settings-method | FlowSOM Endpoints
flowsom.delete | FlowSOM Endpoints
flowsom.delete-method | FlowSOM Endpoints
flowsom.download | FlowSOM Endpoints
flowsom.download-method | FlowSOM Endpoints
flowsom.list | FlowSOM Endpoints
flowsom.list-method | FlowSOM Endpoints
flowsom.new | FlowSOM Endpoints
flowsom.new-method | FlowSOM Endpoints
flowsom.rename | FlowSOM Endpoints
flowsom.rename-method | FlowSOM Endpoints
flowsom.run | FlowSOM Endpoints
flowsom.run-method | FlowSOM Endpoints
flowsom.show | FlowSOM Endpoints
flowsom.show-method | FlowSOM Endpoints
flowsom.status | FlowSOM Endpoints
flowsom.status-method | FlowSOM Endpoints
flowsom.update | FlowSOM Endpoints
flowsom.update-method | FlowSOM Endpoints

## -- G --

gates | Gate Endpoints
gates.apply | Gate Endpoints
gates.apply-method | Gate Endpoints
gates.gatingML_download | Gate Endpoints
gates.gatingML_download-method | Gate Endpoints
gates.gatingML_upload | Gate Endpoints
gates.gatingML_upload-method | Gate Endpoints
gates.list | Gate Endpoints
gates.list-method | Gate Endpoints
gates.show | Gate Endpoints
gates.show-method | Gate Endpoints

## -- H --

helper.channel_ids_from_long_names | Helper Functions
helper.filter_names_to_ids_from_df | Helper Functions
helper_functions | Helper Functions

## -- N --

news | News

## -- O --

optSNE-class | S4 opt-SNE Class

## -- P --

panels | Panel Endpoints
panels.list | Panel Endpoints
panels.list-method | Panel Endpoints
panels.show | Panel Endpoints
panels.show-method | Panel Endpoints
peacoqc | PeacoQC Endpoints
PeacoQC-class | S4 PeacoQC Class
peacoqc.copy_settings | PeacoQC Endpoints
peacoqc.copy_settings-method | PeacoQC Endpoints
peacoqc.list | PeacoQC Endpoints
peacoqc.list-method | PeacoQC Endpoints
peacoqc.new | PeacoQC Endpoints
peacoqc.new-method | PeacoQC Endpoints
peacoqc.rename | PeacoQC Endpoints
peacoqc.rename-method | PeacoQC Endpoints
peacoqc.run | PeacoQC Endpoints
peacoqc.run-method | PeacoQC Endpoints
peacoqc.show | PeacoQC Endpoints
peacoqc.show-method | PeacoQC Endpoints
peacoqc.status | PeacoQC Endpoints
peacoqc.status-method | PeacoQC Endpoints
peacoqc.update | PeacoQC Endpoints
peacoqc.update-method | PeacoQC Endpoints
populations | Population Endpoints
populations.list | Population Endpoints
populations.list-method | Population Endpoints
populations.show | Population Endpoints
populations.show-method | Population Endpoints

## -- S --

sample_tags | Sample Tag Endpoints
sample_tags.download | Sample Tag Endpoints
sample_tags.download-method | Sample Tag Endpoints
sample_tags.upload | Sample Tag Endpoints
sample_tags.upload-method | Sample Tag Endpoints
scales | Scale Endpoints
scales.list | Scale Endpoints
scales.list-method | Scale Endpoints
scales.show | Scale Endpoints
scales.show-method | Scale Endpoints
scales.update | Scale Endpoints
scales.update-method | Scale Endpoints
spade | SPADE Endpoints
SPADE-class | S4 SPADE Class
spade.bubbles_export | SPADE Endpoints
spade.bubbles_export-method | SPADE Endpoints
spade.bubbles_set | SPADE Endpoints
spade.bubbles_set-method | SPADE Endpoints
spade.bubbles_show | SPADE Endpoints
spade.bubbles_show-method | SPADE Endpoints
spade.copy_results | SPADE Endpoints
spade.copy_results-method | SPADE Endpoints
spade.copy_settings | SPADE Endpoints
spade.copy_settings-method | SPADE Endpoints
spade.delete | SPADE Endpoints
spade.delete-method | SPADE Endpoints
spade.download_all | SPADE Endpoints
spade.download_all-method | SPADE Endpoints
spade.download_clusters_table | SPADE Endpoints
spade.download_clusters_table-method | SPADE Endpoints
spade.download_global_boundaries_table | SPADE Endpoints
spade.download_global_boundaries_table-method | SPADE Endpoints
spade.download_gml | SPADE Endpoints
spade.download_gml-method | SPADE Endpoints
spade.download_layout_table | SPADE Endpoints
spade.download_layout_table-method | SPADE Endpoints
spade.download_statistics_tables | SPADE Endpoints
spade.download_statistics_tables-method | SPADE Endpoints
spade.list | SPADE Endpoints
spade.list-method | SPADE Endpoints
spade.new | SPADE Endpoints
spade.new-method | SPADE Endpoints
spade.rename | SPADE Endpoints
spade.rename-method | SPADE Endpoints
spade.run | SPADE Endpoints
spade.run-method | SPADE Endpoints
spade.show | SPADE Endpoints
spade.show-method | SPADE Endpoints
spade.status | SPADE Endpoints
spade.status-method | SPADE Endpoints
spade.update | SPADE Endpoints
spade.update-method | SPADE Endpoints
statistics | Statistic Endpoints
statistics.event_counts | Statistic Endpoints
statistics.event_counts-method | Statistic Endpoints
statistics.general | Statistic Endpoints
statistics.general-method | Statistic Endpoints

## -- T --

tSNE-class | S4 tSNE Class

## -- U --

UMAP-class | S4 UMAP Class
users | User Endpoints
users.list | User Endpoints
users.list-method | User Endpoints
users.show | User Endpoints
users.show-method | User Endpoints
UserSession-class | S4 Cytobank UserSession Class

## -- V --

visne | viSNE Endpoints
viSNE-class | S4 viSNE Class
visne.copy_settings | viSNE Endpoints
visne.copy_settings-method | viSNE Endpoints
visne.delete | viSNE Endpoints
visne.delete-method | viSNE Endpoints
visne.helper.set_populations | viSNE Endpoints
visne.list | viSNE Endpoints
visne.list-method | viSNE Endpoints
visne.new | viSNE Endpoints
visne.new-method | viSNE Endpoints
visne.rename | viSNE Endpoints
visne.rename-method | viSNE Endpoints
visne.run | viSNE Endpoints
visne.run-method | viSNE Endpoints
visne.show | viSNE Endpoints
visne.show-method | viSNE Endpoints
visne.status | viSNE Endpoints
visne.status-method | viSNE Endpoints
visne.update | viSNE Endpoints
visne.update-method | viSNE Endpoints