Bioconductor on the AnVIL compute environment


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Documentation for package ‘AnVIL’ version 1.16.1

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A B D E F G I L O P R S T U misc

-- A --

add_libpaths Utilities for managing library paths
AnVIL-defunct Defunct functions in package 'AnVIL'
AnVIL-deprecated Deprecated AnVIL functionality
as.list.response Process service responses to tibble and other data structures.
av TABLE, DATA, files, bucket, runtime, and disk elements
avbucket TABLE, DATA, files, bucket, runtime, and disk elements
avdata TABLE, DATA, files, bucket, runtime, and disk elements
avdata_import TABLE, DATA, files, bucket, runtime, and disk elements
avdisks TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_backup TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_ls TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_restore TABLE, DATA, files, bucket, runtime, and disk elements
avfiles_rm TABLE, DATA, files, bucket, runtime, and disk elements
avnotebooks Notebook management
avnotebooks_delocalize Notebook management
avnotebooks_localize Notebook management
avruntime TABLE, DATA, files, bucket, runtime, and disk elements
avruntimes TABLE, DATA, files, bucket, runtime, and disk elements
avtable TABLE, DATA, files, bucket, runtime, and disk elements
avtables TABLE, DATA, files, bucket, runtime, and disk elements
avtable_delete_values TABLE, DATA, files, bucket, runtime, and disk elements
avtable_gadget Graphical user interfaces for common AnVIL operations
avtable_import TABLE, DATA, files, bucket, runtime, and disk elements
avtable_import_set TABLE, DATA, files, bucket, runtime, and disk elements
avtable_import_status TABLE, DATA, files, bucket, runtime, and disk elements
avtable_paged TABLE, DATA, files, bucket, runtime, and disk elements
avworkflow Workflow configuration
avworkflows Workflow submissions and file outputs
avworkflow_configuration Defunct functions in package 'AnVIL'
avworkflow_configurations Workflow configuration
avworkflow_configuration_get Workflow configuration
avworkflow_configuration_inputs Workflow configuration
avworkflow_configuration_outputs Workflow configuration
avworkflow_configuration_set Workflow configuration
avworkflow_configuration_template Workflow configuration
avworkflow_configuration_update Workflow configuration
avworkflow_files Workflow submissions and file outputs
avworkflow_gadget Graphical user interfaces for common AnVIL operations
avworkflow_import_configuration Defunct functions in package 'AnVIL'
avworkflow_info Workflow submissions and file outputs
avworkflow_jobs Workflow submissions and file outputs
avworkflow_localize Workflow submissions and file outputs
avworkflow_name Workflow configuration
avworkflow_namespace Workflow configuration
avworkflow_run Workflow submissions and file outputs
avworkflow_stop Workflow submissions and file outputs
avworkspace Workspace management
avworkspaces Workspace management
avworkspace_clone Workspace management
avworkspace_gadget Graphical user interfaces for common AnVIL operations
avworkspace_name Workspace management
avworkspace_namespace Workspace management

-- B --

BINARY_BASE_URL Defunct functions in package 'AnVIL'
browse_workspace Graphical user interfaces for common AnVIL operations

-- D --

delocalize Copy packages, folders, or files to or from google buckets.
Dockstore RESTful services useful for AnVIL developers
Dockstore-class RESTful services useful for AnVIL developers
drs_access_url DRS (Data Repository Service) URL management
drs_cp DRS (Data Repository Service) URL management
drs_stat DRS (Data Repository Service) URL management

-- E --

empty_object RESTful services useful for AnVIL developers

-- F --

flatten Process service responses to tibble and other data structures.
flatten-method Process service responses to tibble and other data structures.

-- G --

gcloud gcloud command line utility interface
gcloud_account gcloud command line utility interface
gcloud_cmd gcloud command line utility interface
gcloud_exists gcloud command line utility interface
gcloud_help gcloud command line utility interface
gcloud_project gcloud command line utility interface
gcloud_storage gcloud command line utility interface
gcloud_storage_buckets gcloud command line utility interface
Gen3Fence Defunct functions in package 'AnVIL'
Gen3Indexd Defunct functions in package 'AnVIL'
Gen3Peregrine Defunct functions in package 'AnVIL'
Gen3Sheepdog Defunct functions in package 'AnVIL'
gsutil gsutil command line utility interface
gsutil_cat gsutil command line utility interface
gsutil_cp gsutil command line utility interface
gsutil_exists gsutil command line utility interface
gsutil_help gsutil command line utility interface
gsutil_ls gsutil command line utility interface
gsutil_pipe gsutil command line utility interface
gsutil_requesterpays gsutil command line utility interface
gsutil_rm gsutil command line utility interface
gsutil_rsync gsutil command line utility interface
gsutil_stat gsutil command line utility interface

-- I --

install Defunct functions in package 'AnVIL'

-- L --

Leonardo RESTful services useful for AnVIL developers
Leonardo-class RESTful services useful for AnVIL developers
localize Copy packages, folders, or files to or from google buckets.

-- O --

operations RESTful services useful for AnVIL developers
operations-method RESTful services useful for AnVIL developers

-- P --

print.avworkflow_configuration Workflow configuration
print.repository_stats Deprecated AnVIL functionality

-- R --

Rawls RESTful services useful for AnVIL developers
Rawls-class RESTful services useful for AnVIL developers
repositories Defunct functions in package 'AnVIL'
repository Defunct functions in package 'AnVIL'
repository_stats Deprecated AnVIL functionality
Response Process service responses to tibble and other data structures.

-- S --

schemas RESTful services useful for AnVIL developers
schemas-method RESTful services useful for AnVIL developers
Service RESTful service constructor
Service-class RESTful services useful for AnVIL developers
Services RESTful services useful for AnVIL developers
show-method RESTful services useful for AnVIL developers
str-method Process service responses to tibble and other data structures.

-- T --

tags RESTful services useful for AnVIL developers
Terra RESTful services useful for AnVIL developers
Terra-class RESTful services useful for AnVIL developers

-- U --

utilities Utilities for managing library paths

-- misc --

$-method RESTful services useful for AnVIL developers
.DollarNames.Service RESTful services useful for AnVIL developers
.gadget_run Functions to implement AnVIL gadget interfaces