| Last modified 2025-06-12 |
Use HISE SDK Methods
At a Glance
SDK methods are available in R and Python to read and download data to your instances, store intermediate files, schedule notebooks, manage IDE state, and save results, visualizations, or abstractions.
 | Abbreviations Key | |||
| ad | AnnData (annotated data [Python/R package for storing spatial matrices]) | HTO | hashtag oligo | |
| ADT | antibody-derived tags | IDE | integrated development environment | |
| c | concatenate | QC | quality control | |
| HDF5 | hierarchical data format, version 5 | SDK | software development kit | |
| HISE | Human Immune System Explorer | stderr | standard error | |
| UMI | unique molecular identifier |
When using an import statement like |
Reader Methods
Following is a list of methods to read or download data to your IDE instance.
| Method Name | Description |
| hisepy.hise_file() | Creates and returns a single hise_file object. |
| hisepy.cache_files() | Downloads the specified files and stores them locally in a cache directory, without loading their contents into memory. |
| hisepy.query_files() | Searches for files in HISE based on user-defined criteria, and returns metadata (but not file contents) for the matching files. |
| hisepy.cache_fileset() | Downloads and caches metadata for a file set (a group of files) without loading file contents. |
| hisepy.list_filesets() | Retrieves a list of available filesets, including their identifiers and basic metadata. |
| hisepy.get_file_descriptors() | Retrieves file descriptors based on the user's query, as in this example:
|
| hisepy.read_files() | Reads the contents of a list of file IDs into a hise_file object.Note: Only one parameter per function call is allowed. |
| hisepy.read_samples() | Reads or searches the SampleStatus materialized view. Here's an example:
|
| hisepy.read_subjects() | Reads or searches the
|
| Method Name | Description |
| cacheFiles() | Downloads the specified files and stores them locally in a cache directory, without loading their contents into memory. |
| getFileDescriptors() | Retrieves file descriptors based on the user's query. |
| readFiles() | Reads the contents of a list of file IDs into a hise_file object.Note: Only one parameter per function call is allowed. |
| readSamples() | Reads or searches the SampleStatus materialized view. |
| readSubjects() | Reads or searches the
|
Upload Methods
The following methods help you upload results to the collaboration space.
| Method Name | Description |
| get_study_spaces() | Returns a list of studies the user can access. |
| upload_files() | Uploads files to a specified project or study. Can be used to save intermediate files that someone else can use as their starting point for further analysis. |
| save_visualization() | Saves a Plotly object to a specified study. |
| load_visualization() | Loads a Plotly visualization that was saved to a study. |
| save_dash_app() | Given a Dash app consisting of an entry point named app.py and a list of supporting files, uploads and deploys that app to HISE as a visualization in the specified study. |
| save_static_image() | Saves a static image (such as a PNG or JPEG file) to a specified study for documentation or sharing. |
| get_default_project() | Retrieves the default project for the current user or session. |
| get_default_store() | Retrieves the default data store for the current user or session. |
| get_files_for_query() | Returns a list of files that match the specified query parameters within a study or project. |
| get_trace() | Retrieves detailed trace or log information for a specific analysis, process, or workflow. |
| set_default_project() | Sets the default project for the current user or session. |
| set_default_store() | Sets the default data store for the current user or session. |
| Method Name | Description |
| getStudySpace() | Returns a list of studies the user can access. |
| uploadFiles() | Uploads files to a specified project or study. Can be used to save intermediate files that someone else can use as their starting point for further analysis. |
| loadVisualization() | Loads a Plotly visualization that was saved to a study. Note: This function might be buggy. If so, file a help ticket by clicking the Support button in the upper-right corner of this page. |
| saveVisualization() | Saves a Plotly object to a specified study. Note: This function might be buggy. If so, file a help ticket by clicking the Support button in the upper-right corner of this page. |
| uploadFiles() | Uploads files to a specified project or study. |
Project Store
The following methods let you interact with the Project Store.
| Method Name | Description |
| delete_file_in_project_store() | Deletes a file in the project store, provided it's not otherwise in use. |
| download_file_from_project_store() | Downloads a given file to the user's IDE. |
| list_files_in_project_stores() | Returns a list of files present in a given project store. |
| list_project_stores() | Lists all project stores the user can access. |
| promote_file_in_project_store() | Marks a file in a project store to be promoted to the permanent store. After promotion, the file is managed in the permanent store and is no longer returned in a list_files_in_project_stores() call. |
| undo_delete_in_project_store() | Undoes the file delete action, provided the call is executed within the file's retention period. |
| undo_promote_file_in_project_store() | Undoes the promotion action, provided the file has not already been moved to the permanent store. After the undo call is executed, the file again becomes visible in a call to list_files_in_project_store(). |
| Method Name | Description |
| deleteFileInProjectStore() | Deletes a file in the project store, so long as it is not otherwise in use. |
| downloadFileFromProjectStore() | Downloads a given file onto a user's IDE. |
| listFilesInProjectStores() | Returns information about what files are present in a given project store. |
| listProjectStores() | Lists all project stores a user has access to. |
| promoteFileInProjectStore() | After promotion, the file is managed in the permanent store and is no longer returned in a listFilesInProjectStore() call. |
| undoDeleteInProjectStore() | Undoes the file delete action, so long as it is within the file's retention period. |
| undoPromoteFileInProjectStore() | Undoes the promotion action, so long as the file has not already been moved to the permanent store. The file will once again be visible via listFilesInProjectStore(). |
Private Folders
The following methods let you interact with private folders.
| Method Name | Description |
| create_private_folder() | Creates a new private folder. |
| delete_file_in_private_folder() | Deletes a file from a private folder. |
| delete_private_folder() | Deletes an existing private folder. |
| download_from_private_folder() | Downloads a file from a private folder to your local working directory. |
| find_private_folder_of_file() | Returns the name or identifier of the private folder containing the specified file. |
| list_files_in_all_private_folders() | Returns a data.frame of all private folders and files that are within each. |
| list_files_in_private_folder() | Lists files inside a given private folder. |
| move_file_in_private_folder() | Moves a file between private folders. |
| rename_file_in_private_folder() | Renames a file in a private folder. |
| upload_file_to_private_folder() | Uploads a file to a private folder. |
Skip to main content Method Name Description... Body:
| Method Name | Description |
| createPrivateFolder() | Creates a new private folder. |
| deleteFileInPrivateFolder() | Deletes a file from a private folder. |
| deletePrivateFolder() | Deletes an existing private folder. |
| downloadFromPrivateFolder() | Downloads a file from a private folder to your local working directory. |
| listFilesInAllPrivateFolders() | Lists all folders that belong to this user and the files inside them. |
| listFilesInPrivateFolder() | Lists files inside a given private folder. |
| MoveFileInPrivateFolder() | Moves a file between private folders. |
| renameFileInPrivateFolder() | Renames a file in a private folder. |
| uploadFileToPrivateFolder() | Uploads a file to a private folder. |
IDE Management Methods
The following method stops an IDE instance.
| Method Name | Description |
| stop_ide() | Stops the active instance from which this method is invoked. |
| Method Name | Description |
| stopIDE() | Stops the active instance from which this method is invoked. |
Lookup Methods
Lookup methods are used to find appropriate field names for querying, and to look up the unique values for each field name.
| Method Name | Description |
| lookup_queryable_fields() | Returns a list of fields used for creating queries. |
| lookup_unique_entries() | Returns unique values for a given field. |
| Method Name | Description |
| lookupQueryableFields() | Returns a list of fields used for creating queries. |
| lookupUniqueEntries() | Returns unique values for a given field. |
H5 Weaver
The following R functions are for reading, rearranging, and writing 10x-compatible HDF5 files.
| Method Name | Description |
| add_cell_ids | Adds cell IDs to an h5_list object. |
| add_h5_list_adt_results | Adds ADT results to an h5_list. |
| add_h5_list_hash_results | Adds cell hashing results to an h5_list object. |
| add_h5_transposed_matrix | Adds a transposed version of a matrix to an .h5 file. |
| add_well_metadata | Adds well metadata. |
| append_ext_h5_character | Appends character values to an existing HDF5 string dataset. |
| cat_h5_list | Concatenates two h5_list objects. |
| choose_chunk_size | Select a reasonable chunk size for an HDF5 dataset object. |
| choose_integer_bits | Decides how many bits to use to store integer values in an HDF5 dataset object. |
| convert_char_na | Converts NA character entries to actual NAs. |
| convert_char_na_recursive | Converts all NA character values to actual NAs recursively. |
| create_ext_h5_character | Creates an extensible character HDF5 dataset. |
| create_ext_h5_float | Creates an extensible float HDF5 dataset. |
| create_ext_h5_uint | Creates an extensible unsigned integer HDF5 dataset. |
| get_list_path | Retrieves an object from a list using path-style targeting. |
| h5_attr_list | Generates a set of attributes based on 10x Genomics defaults. |
| h5_list_add_dgCMatrix | Adds a sparse matrix to an h5_list containing 10x Genomics data. |
| h5_list_add_mita_umis | Adds mitochondrial gene UMI counts to an h5_list object. |
| h5_list_cell_metadata | Extracts a data.frame of cell metadata from an h5_list object. |
| h5_list_convert_from_dgCMatrix | Converts the matrix in an h5_list from a sparse matrix back to its original structure. |
| h5_list_convert_to_dgCMatrix | Converts the matrix in an h5_list from 10x Genomics data to a sparse matrix. |
| h5_list_transpose | Transposes an h5_list object. |
| h5dims | Gets dimensions of an object in an HDF5 file. |
| h5dump | Dumps all objects from an HDF5 file to a list. |
| h5exists | Checks if an object exists in an HDF5 file. |
| h5ls | Lists objects in an HDF5 file. |
| qc_aligned_barplot | Generates a baseline-aligned barplot for two categorical metrics. |
| qc_cutoff_barplot | Generates a QC barplot for a metric at multiple cutoffs. |
| qc_flip | Flips the orientation of a data.frame and returns as a list. |
| qc_frac_hist_plot | Generates a QC histogram plot for a single fractional metric. |
| qc_hist_plot | Generates a QC histogram plot for a single metric. |
| qc_stacked_barplot | Generates a stacked barplot for two categorical metrics. |
| qc_table | Renders a custom-formatted table for QC metrics. |
| qc_violin_plot | Generates a QC violin plot for a metric, grouped by a categorical metadata column. |
| read_h5_cell_meta | Reads .h5 cell metadata. |
| read_h5_dgCMatrix | Reads the /matrix from an .h5 file as a sparse matrix. |
| read_h5_feature_meta | Reads .h5ad feature metadata. |
| read_tenx_metrics | Reads and corrects formatting of a 10x metics_summary.csv file. |
| reduce_h5_list | Reduces a list-of-lists of h5_list objects to a single, concatenated object. |
| set_list_path | Sets a list value using path-style targeting. |
| split_h5_list_by_hash | Splits a 10x HDF5 file based on HTOparser results. |
| stm | Writes a stderr message with a leading data/time stamp. |
| strip_1d_array_recursive | Recursively traverses a list and converts into vectors any one-dimensional array elements it contains. |
| subset_h5_list_by_observations | Subsets an h5_list object based on a set of observations. |
| varibow | Generates a rainbow palette with variations in saturation and value. |
| write_10x_h5_container | Generates an empty HDF5 container to store RNA-seq count data in 10x format. |
| write_h5_list | Writes an h5_list, as created by rhddf5::h5dump(), to an .h5 file. |
Abstraction Methods
Below are a few SDK methods to help you work with abstractions.
| Method Name | Description |
| get_result_files | Retrieves a list of result files generated by an analysis or workflow. |
| result_filetype_to_guid | Returns the GUID associated with the specified result file type. |
| save_abstraction | Saves a visualization template to the IDE user's account. |
Utilities
Following is a brief list of utility methods.
| Method Name | Description |
| _dict_to_df | Converts a data dictionary into a pandas DataFrame for further analysis or processing. |
| hise_file_to_df | Converts the contents of a hise_file object into a pandas DataFrame. |
| sample_to_df | Converts sample-level metadata or data into a pandas DataFrame. |
| subject_to_df | Converts subject-level metadata or data into a pandas DataFrame. |
Related Resources