### Get All Sample Lists with Detailed Projection

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Retrieves all available sample lists with detailed information. The output is a pandas DataFrame.

```python
df1 = sl.get_all_sample_lists(projection="DETAILED")
df1
```

--------------------------------

### Info

Source: https://pybioportal.readthedocs.io/en/latest/modules.html

Function to get general information about the server.

```APIDOC
## get_info()

### Description
Retrieves general information about the cBioPortal server.

### Method
GET

### Endpoint
/info
```

--------------------------------

### Get All Molecular Profiles

Source: https://pybioportal.readthedocs.io/en/latest/molecular_profiles.html

Retrieve all available molecular profiles. Displays the first 5 rows of the resulting DataFrame.

```python
df1 = mf.get_all_molecular_profiles()
df1.head(5)
```

--------------------------------

### Get a Specific Sample List by ID

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Fetches a single sample list using its unique identifier. The result is a pandas DataFrame.

```python
df2 = sl.get_sample_list(sample_list_id="brca_tcga_cna")
df2
```

--------------------------------

### Get All Sample IDs in a Sample List

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Retrieves all sample IDs belonging to a specified sample list. The output is a pandas DataFrame.

```python
df3 = sl.get_all_sample_ids_in_sample_list(sample_list_id="brca_tcga_cna")
df3
```

--------------------------------

### Get All Sample Lists in a Study

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Fetches all sample lists associated with a specific study ID, including detailed information. The result is a pandas DataFrame.

```python
df5 = sl.get_all_sample_lists_in_study(study_id="brca_tcga",projection="DETAILED")
df5
```

--------------------------------

### Example Output of get_info()

Source: https://pybioportal.readthedocs.io/en/latest/info.html

This snippet shows the expected output format and content when calling get_info() and printing its columns. It includes details like portal version, database version, and git commit information.

```text
portalVersion: 5.4.7-dirty-SNAPSHOT
dbVersion: 2.13.1
gitBranch: d4b06559c81a99911d620107113b2acf0e40523e
gitCommitId: d4b06559c81a99911d620107113b2acf0e40523e
gitCommitIdDescribe: v5.4.7-dirty
gitCommitIdDescribeShort: v5.4.7-dirty
gitCommitMessageFull: Merge pull request #10453 from cBioPortal/front...
gitCommitMessageShort: Merge pull request #10453 from cBioPortal/front...
gitCommitMessageUserEmail: 15748980+dippindots@users.noreply.github.com
gitCommitMessageUserName: Gaofei Zhao
gitDirty: True
```

--------------------------------

### Get All Samples in a Study

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Use `get_all_samples_in_study` to retrieve all samples belonging to a specific study. This is useful for a broad overview of all samples within a research study.

```python
df4 = sp.get_all_samples_in_study(study_id="brca_tcga")
df4
```

--------------------------------

### Get All Study IDs

Source: https://pybioportal.readthedocs.io/en/latest/treatments.html

Fetches all study IDs to be used in subsequent treatment queries. This is a prerequisite for most treatment-related API calls.

```python
from pybioportal import studies as std
studies = std.get_all_studies(projection="DETAILED")
std_ids = studies["studyId"].to_list()
print(f"First Study IDs of {len(std_ids)}: {std_ids[0:5]}")
```

--------------------------------

### Get All Molecular Profiles in a Study with Custom Sorting

Source: https://pybioportal.readthedocs.io/en/latest/molecular_profiles.html

Retrieve all molecular profiles within a specific study, sorted by their description. Displays the first 5 rows of the resulting DataFrame.

```python
df4 = mf.get_all_molecular_profiles_in_study(study_id="brca_tcga", sortBy="description")
df4.head(5)
```

--------------------------------

### Get all gene panels

Source: https://pybioportal.readthedocs.io/en/latest/gene_panels.html

Retrieve a DataFrame containing all available gene panels. Use `.head(10)` to display the first 10 entries.

```python
df1 = gp.get_all_gene_panels()
df1.head(10)
```

--------------------------------

### Get All Genes by Keyword

Source: https://pybioportal.readthedocs.io/en/latest/genes.html

Fetch all genes matching a specific keyword, such as a gene symbol. This is useful for searching for genes when you know part of their name.

```python
df1a = gns.get_all_genes(keyword = "BRCA1")
df1a
```

--------------------------------

### Get cBioPortal Instance Information

Source: https://pybioportal.readthedocs.io/en/latest/info.html

Retrieves information about the running cBioPortal instance. This function is useful for understanding the environment and version details of the portal.

```python
from pybioportal.info import get_info
get_info()
```

--------------------------------

### Get All Samples for a Patient in a Study

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Use `get_all_samples_of_patient_in_study` to retrieve all samples associated with a specific patient within a given study. This helps in analyzing all data points for a single patient.

```python
df3 = sp.get_all_samples_of_patient_in_study(study_id="brca_tcga", patient_id="TCGA-AR-A1AR")
df3
```

--------------------------------

### Get Generic Assay Metadata by Molecular Profile ID

Source: https://pybioportal.readthedocs.io/en/latest/generic_assays.html

Retrieves all generic assay metadata for a single molecular profile ID. The output includes stableId, entityType, gene symbol, and phosphosite.

```python
df2 = ga.get_generic_assay_meta_by_molecular_profile_id("brca_tcga_phosphoprotein_quantification")
df2
```

--------------------------------

### Get All Molecular Data in a Profile for a Sample List

Source: https://pybioportal.readthedocs.io/en/latest/molecular_data.html

Retrieve all molecular data within a specific molecular profile for a given sample list and Entrez gene ID. This is useful for comprehensive analysis within a defined subset of data.

```python
df2 = md.get_all_molecular_data_in_molecular_profile(molecular_profile_id="brca_tcga_rppa",
                                                     sample_list_id="brca_tcga_all",
                                                     entrez_gene_id="675")
df2
```

--------------------------------

### Get All Patient Clinical Data for a Study

Source: https://pybioportal.readthedocs.io/en/latest/clinical_data.html

Fetches all available patient-level clinical data for a given study ID. This is useful for exploring all data points associated with patients in a specific cohort.

```python
df2a = cd.get_all_clinical_data_in_study("acc_tcga", clinical_data_type="PATIENT")
df2a
```

--------------------------------

### Get a Specific Sample in a Study

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Use `get_sample_in_study` to retrieve details for a single, specific sample within a study, identified by its `sample_id`. This is useful for detailed inspection of individual samples.

```python
df5 = sp.get_sample_in_study(study_id="brca_tcga",sample_id="TCGA-AR-A1AR-01")
df5
```

--------------------------------

### Fetch All Patients in a Specific Study with Detailed Projection

Source: https://pybioportal.readthedocs.io/en/latest/patients.html

Get all patients belonging to a particular study, such as 'brca_tcga', with a 'DETAILED' projection. This provides extensive metadata for each patient within the study.

```python
df3 = pts.get_all_patients_in_study(study_id="brca_tcga", projection="DETAILED")
df3
```

--------------------------------

### Get Clinical Data for a Specific Sample in a Study

Source: https://pybioportal.readthedocs.io/en/latest/clinical_data.html

Fetches all clinical data points for a specific sample within a given study. This is useful for detailed analysis of an individual sample's clinical profile.

```python
df5 = cd.get_all_clinical_data_of_sample_in_study(study_id="msk_met_2021", sample_id="P-0000004-T01-IM3")
df5
```

--------------------------------

### Get Generic Assay Data in Molecular Profile

Source: https://pybioportal.readthedocs.io/en/latest/generic_assay_data.html

Retrieves generic assay data for a specific molecular profile and assay. Use this when you need to filter data by both a molecular profile and a specific assay identifier.

```python
import pandas as pd
import bioportal.generic_assay_data as gad

df3 = gad.get_generic_assay_data_in_molecular_profile(molecular_profile_id = "brca_tcga_phosphoprotein_quantification",
                                                      generic_assay_stable_id = "TULP4_pS563")
df3
```

--------------------------------

### Fetch Molecular Data by Gene and Profile IDs

Source: https://pybioportal.readthedocs.io/en/latest/molecular_data.html

Retrieve molecular data for specified Entrez gene IDs and molecular profile IDs. This is useful for getting a broad overview of gene expression across different profiles.

```python
from pybioportal import molecular_data as md

df1a = md.fetch_molecular_data(entrez_gene_ids=["672","675"],
                               molecular_profile_ids=["brca_tcga_mrna", "acc_tcga_rna_seq_v2_mrna"])
df1a
```

--------------------------------

### Get Generic Assay Metadata by Assay ID

Source: https://pybioportal.readthedocs.io/en/latest/generic_assays.html

Fetches metadata for a single generic assay using its unique stable ID. The returned data includes stableId, entityType, gene symbol, and phosphosite.

```python
df3 = ga.get_generic_assay_meta_by_id("TULP4_pS563")
df3
```

--------------------------------

### Get Generic Assay Data in Molecular Profile

Source: https://pybioportal.readthedocs.io/en/latest/generic_assay_data.html

Retrieves specific generic assay data for a given molecular profile and a single generic assay stable ID. The 'projection' parameter determines the detail level of the returned data.

```python
pybioportal.generic_assay_data.get_generic_assay_data_in_molecular_profile(_molecular_profile_id_ , _generic_assay_stable_id_ , _projection ='SUMMARY'_)
```

--------------------------------

### Get Specific Cancer Type

Source: https://pybioportal.readthedocs.io/en/latest/cancer_types.html

Retrieves a DataFrame with detailed information for a specific cancer type, identified by its cancer_type_id. Use this to get in-depth data about a particular cancer.

```python
df2 = ct.get_cancer_type(cancer_type_id="brca")
df2
```

--------------------------------

### Get Gene Information by Symbol or ID

Source: https://pybioportal.readthedocs.io/en/latest/genes.html

Fetch detailed information for a specific gene using its Hugo Gene Symbol or Entrez Gene ID. This is the primary way to get data for a single known gene.

```python
df2 = gns.get_gene("BRCA1")
df2
```

--------------------------------

### Sample Lists

Source: https://pybioportal.readthedocs.io/en/latest/modules.html

Functions for fetching and retrieving sample list information.

```APIDOC
## fetch_sample_lists()

### Description
Fetches sample lists.

### Method
POST

### Endpoint
/sample_lists/fetch

## get_all_sample_ids_in_sample_list()

### Description
Retrieves all sample IDs within a specific sample list.

### Method
GET

### Endpoint
/sample_lists/{sample_list_id}/samples

## get_all_sample_lists()

### Description
Retrieves all available sample lists.

### Method
GET

### Endpoint
/sample_lists

## get_all_sample_lists_in_study()

### Description
Retrieves all sample lists within a specific study.

### Method
GET

### Endpoint
/studies/{study_id}/sample_lists

## get_sample_list()

### Description
Retrieves a specific sample list by its identifier.

### Method
GET

### Endpoint
/sample_lists/{sample_list_id}
```

--------------------------------

### Samples

Source: https://pybioportal.readthedocs.io/en/latest/modules.html

Functions for fetching and retrieving sample information.

```APIDOC
## fetch_samples()

### Description
Fetches sample information.

### Method
POST

### Endpoint
/samples/fetch

## get_all_samples_in_study()

### Description
Retrieves all samples within a specific study.

### Method
GET

### Endpoint
/studies/{study_id}/samples

## get_all_samples_of_patient_in_study()

### Description
Retrieves all samples belonging to a specific patient within a study.

### Method
GET

### Endpoint
/studies/{study_id}/patients/{patient_id}/samples

## get_sample_in_study()

### Description
Retrieves a specific sample within a study by its ID.

### Method
GET

### Endpoint
/studies/{study_id}/samples/{sample_id}

## get_samples_by_keyword()

### Description
Retrieves samples matching a keyword search.

### Method
GET

### Endpoint
/samples/search
```

--------------------------------

### Server running status

Source: https://pybioportal.readthedocs.io/en/latest/modules.html

Function to get the server's running status.

```APIDOC
## get_server_status()

### Description
Retrieves the current running status of the server.

### Method
GET

### Endpoint
/status
```

--------------------------------

### Import Sample Lists Module

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Imports the sample_lists module from the pybioportal library.

```python
from pybioportal import sample_lists as sl
```

--------------------------------

### Fetch Samples by Unique Keys

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Use `fetch_samples` to retrieve specific samples using their unique keys. This is useful when you know the exact identifiers of the samples you need.

```python
df2c = sp.fetch_samples(unique_sample_keys=["VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ",
                                            "VENHQS1CNi1BMElRLTAxOmJyY2FfdGNnYV9wdWI",
                                            "VENHQS1CSC1BMUZELTAxOmJyY2FfdGNnYQ"])
df2c
```

--------------------------------

### Get all clinical attributes

Source: https://pybioportal.readthedocs.io/en/latest/clinical_attributes.html

Fetch all available clinical attributes across all studies. This can be useful for an overview of the data available.

```python
df1 = ca.get_all_clinical_attributes()
df1
```

--------------------------------

### Fetch Multiple Sample Lists by IDs

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Retrieves multiple sample lists by providing a list of their IDs and a projection. The output is a pandas DataFrame.

```python
df4 = sl.fetch_sample_lists(sample_list_ids=["brca_tcga_cna", "brca_tcga_mrna"], projection="DETAILED")
df4
```

--------------------------------

### Get Tags for a Study

Source: https://pybioportal.readthedocs.io/en/latest/studies.html

Retrieves tags associated with a given study ID. The output is a pandas DataFrame containing the tags.

```python
df3 = std.get_tags_of_study(study_id="bowel_colitis_msk_2022")
df3
```

--------------------------------

### Get Single Study by ID

Source: https://pybioportal.readthedocs.io/en/latest/studies.html

Fetches detailed information for a specific study identified by its 'study_id'. The result is a pandas DataFrame.

```python
df2 = std.get_study(study_id="brca_tcga")
df2
```

--------------------------------

### Fetch Molecular Data by Profile, Gene, and Sample

Source: https://pybioportal.readthedocs.io/en/latest/molecular_data.html

Fetches molecular data for specified molecular profiles, entrez gene IDs, and sample IDs. Useful for targeted data retrieval.

```python
df3 = md.fetch_all_molecular_data_in_molecular_profile(molecular_profile_id = "brca_tcga_rppa",
                                                       entrez_gene_ids = ["672","675"],
                                                       sample_ids = ["TCGA-AR-A1AR-01","TCGA-BH-A1EO-01"])
df3
```

--------------------------------

### Import PyBioPortal Samples Module

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Imports the samples module from the PyBioPortal library. This is a prerequisite for using any sample-related functions.

```python
from pybioportal import samples as sp
```

--------------------------------

### Get Specific Cancer Type

Source: https://pybioportal.readthedocs.io/en/latest/cancer_types.html

Retrieves detailed information for a single, specific cancer type using its unique ID.

```APIDOC
## GET /cancer_types/{cancer_type_id}

### Description
Retrieves detailed information about a specific cancer type from cBioPortal using its ID.

### Method
GET

### Endpoint
/cancer_types/{cancer_type_id}

### Parameters
#### Path Parameters
- **cancer_type_id** (string) - Required - Cancer Type ID (e.g., “brca”).

### Response
#### Success Response (200)
- **DataFrame** - A pandas DataFrame containing information about the specific cancer type, including 'name', 'dedicatedColor', 'shortName', 'parent', and 'cancerTypeId'.

### Response Example
```json
{
  "example": "[DataFrame with specific cancer type information]"
}
```
```

--------------------------------

### pybioportal.sample_lists.get_all_sample_lists

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Retrieves all available sample lists with options for projection, sorting, and pagination.

```APIDOC
## get_all_sample_lists

### Description
Retrieves all sample lists available in the system. Supports filtering and sorting.

### Method
Not applicable (Python function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **projection** (_str_) – Optional - Level of detail of the response. Possible values: "DETAILED", "ID", "META", "SUMMARY" (default).
* **direction** (_str_) – Optional - Direction of the sort. Possible values: "ASC" (default), "DESC".
* **pageNumber** (_int_) – Optional - Page number of the result list. Minimum value is 0.
* **pageSize** (_int_) – Optional - Page size of the result list. Minimum value is 1, maximum value is 10000000.
* **sortBy** (_str_) – Optional - Name of the property that the result list is sorted by. Possible values: "category", "description", "name", "sampleListId", "studyId".

### Returns
A DataFrame containing sample lists.

### Return Type
pandas.DataFrame
```

--------------------------------

### Get All Cancer Types

Source: https://pybioportal.readthedocs.io/en/latest/cancer_types.html

Retrieves a list of all cancer types available in cBioPortal. Supports filtering and sorting through various parameters.

```APIDOC
## GET /cancer_types

### Description
Retrieves a list of all cancer types from cBioPortal. This function allows for sorting and pagination of the results.

### Method
GET

### Endpoint
/cancer_types

### Parameters
#### Query Parameters
- **direction** (string) - Optional - Direction of the sort. Possible values: "ASC", "DESC". Defaults to "ASC".
- **pageNumber** (integer) - Optional - Page number of the result list. Minimum value is 0. Defaults to 0.
- **pageSize** (integer) - Optional - Page size of the result list. Minimum value is 1, maximum value is 10000000. Defaults to 10000000.
- **projection** (string) - Optional - Level of detail of the response. Possible values: "DETAILED", "ID", "META", "SUMMARY". Defaults to "SUMMARY".
- **sortBy** (string) - Optional - Name of the property that the result list is sorted by.

### Response
#### Success Response (200)
- **DataFrame** - A pandas DataFrame containing the list of cancer types with columns like 'name', 'dedicatedColor', 'shortName', 'parent', and 'cancerTypeId'.

### Response Example
```json
{
  "example": "[DataFrame with cancer type information]"
}
```
```

--------------------------------

### Fetch Samples by Sample List IDs

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Retrieves samples using a list of pre-defined sample list IDs. This is a convenient way to fetch related sets of samples from different data types or studies.

```python
df2b = sp.fetch_samples(sample_list_ids=["brca_tcga_cna", "brca_tcga_mrna", "brca_tcga_pub_cna"])
df2b
```

--------------------------------

### Import Server Running Status Module

Source: https://pybioportal.readthedocs.io/en/latest/server_running_status.html

Import the server_running_status module from the pybioportal library. This is a prerequisite for using its functions.

```python
from pybioportal import server_running_status as srs
```

--------------------------------

### Get metadata clinical attributes for a study

Source: https://pybioportal.readthedocs.io/en/latest/clinical_attributes.html

Retrieve metadata-level clinical attributes for a specific study. The 'META' projection is used for this purpose.

```python
df3b = ca.get_all_clinical_attributes_in_study(study_id="brca_tcga", projection="META")
df3b
```

--------------------------------

### Get Specific Molecular Profile by ID

Source: https://pybioportal.readthedocs.io/en/latest/molecular_profiles.html

Fetch a single molecular profile using its unique ID. Displays the entire resulting DataFrame.

```python
df2 = mf.get_molecular_profile("gbm_tcga_pan_can_atlas_2018_armlevel_cna")
df2
```

--------------------------------

### Get detailed clinical attributes for a study

Source: https://pybioportal.readthedocs.io/en/latest/clinical_attributes.html

Fetch detailed clinical attributes for a specific study. The 'DETAILED' projection provides more comprehensive information.

```python
df3a = ca.get_all_clinical_attributes_in_study(study_id="brca_tcga", projection="DETAILED")
df3a
```

--------------------------------

### Import PyBioPortal Treatments Module

Source: https://pybioportal.readthedocs.io/en/latest/treatments.html

Import the treatments module from the pybioportal library.

```python
from pybioportal import treatments as trt
```

--------------------------------

### Fetch Samples by Keyword

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Retrieves a DataFrame of samples associated with a specific keyword. This is useful for broad searches across studies.

```python
df1 = sp.get_samples_by_keyword(keyword="TCGA")
df1
```

--------------------------------

### Get All Genes by Alias

Source: https://pybioportal.readthedocs.io/en/latest/genes.html

Retrieve all genes associated with a given alias. This function helps find genes when you only know one of their alternative names.

```python
df1b = gns.get_all_genes(alias = "FANCS")
df1b
```

--------------------------------

### pybioportal.samples.get_samples_by_keyword

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Retrieves all samples that match a given keyword. Supports sorting, pagination, and projection options.

```APIDOC
## get_samples_by_keyword

### Description
Retrieves all samples matching a keyword. The keyword applies to the study ID. Supports sorting, pagination, and projection options.

### Method
`pybioportal.samples.get_samples_by_keyword`

### Parameters
#### Path Parameters
None

#### Query Parameters
* **keyword** (str) - Optional - Search keyword that applies to the study ID.
* **direction** (str) - Optional - Direction of the sort. Possible values: `"ASC"` (default), `"DESC"`.
* **pageNumber** (int) - Optional - Page number of the result list. Minimum value is 0.
* **pageSize** (int) - Optional - Page size of the result list. Minimum value is 1, maximum value is 10000000.
* **projection** (str) - Optional - Level of detail of the response. Possible values: `"DETAILED"`, `"ID"`, `"META"`, `"SUMMARY"` (default).
* **sortBy** (str) - Optional - Name of the property that the result list is sorted by. Possible values: `"sampleId"`, `"sampleType"`.

### Request Example
```python
samples = pybioportal.samples.get_samples_by_keyword(
    keyword="brca_tcga",
    sortBy="sampleId"
)
```

### Response
#### Success Response (200)
Returns a pandas.DataFrame containing samples matching the keyword.

#### Response Example
```
# DataFrame structure depends on the projection used.
# Example for SUMMARY projection:
#      SAMPLE_ID  PATIENT_ID  STUDY_ID
# 0  TCGA-AR-A1AR-01  TCGA-AR-A1AR  brca_tcga
```
```

--------------------------------

### Fetch Generic Assay Data by Sample IDs

Source: https://pybioportal.readthedocs.io/en/latest/generic_assay_data.html

Fetches generic assay data for specified molecular profile, assay IDs, and sample IDs. This is useful for retrieving data for a targeted set of samples.

```python
df1a = gad.fetch_generic_assay_data_in_molecular_profile(molecular_profile_id="brca_tcga_phosphoprotein_quantification",
                                                         generic_assay_stable_ids = ["TULP4_pS563", "TEP1_pS397"],
                                                         sample_ids = ["TCGA-C8-A130-01", "TCGA-C8-A134-01"])
df1a
```

--------------------------------

### Fetch Sample Level Treatments by Treatment Time and Name

Source: https://pybioportal.readthedocs.io/en/latest/treatments.html

Fetches sample-level treatment data filtered by treatment time ('Pre' or 'Post') and treatment name for a specific study. The output is a pandas DataFrame.

```python
filter2b = {"sampleTreatmentFilters": {
    "filters": [
      {
        "filters": [
          {
            "time": "Pre",
            "treatment": "Palbociclib"
          },
          {
            "time": "Post",
            "treatment": "Palbociclib"
          }
        ]
      }
    ]
  },
  "studyIds": ["brca_tcga"]}

df2b = trt.fetch_all_sample_level_treatments(study_view_filter=filter2b)
df2b
```

--------------------------------

### Get All Studies with Keyword Projection

Source: https://pybioportal.readthedocs.io/en/latest/studies.html

Retrieves a detailed list of all studies matching the keyword 'TCGA'. The output is a pandas DataFrame containing study metadata.

```python
df1 = std.get_all_studies(keyword="TCGA", projection="DETAILED")
df1
```

--------------------------------

### Fetch Generic Assay Data by Sample List ID

Source: https://pybioportal.readthedocs.io/en/latest/generic_assay_data.html

Fetches generic assay data for a specified molecular profile and assay IDs using a predefined sample list ID. This is useful for retrieving data for a broader set of samples defined by a list.

```python
df1b = gad.fetch_generic_assay_data_in_molecular_profile(molecular_profile_id="brca_tcga_phosphoprotein_quantification",
                                                         generic_assay_stable_ids = ["TULP4_pS563", "TEP1_pS397"],
                                                         sample_list_id = "brca_tcga_all")
df1b
```

--------------------------------

### Fetch Samples by Specific Identifiers

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Fetches samples using a list of sample IDs, grouped by study ID. This method allows for precise data retrieval from multiple studies simultaneously.

```python
df2a = sp.fetch_samples(sample_identifiers=[
                                            {"sample_ids": ["TCGA-AR-A1AR-01","TCGA-BH-A1EO-01","TCGA-BH-A1ES-01"],
                                             "study_id": "brca_tcga"},
                                            {"sample_ids": ["TCGA-A2-A0T2-01","TCGA-A2-A04P-01"],
                                             "study_id": "brca_tcga_pub"}
                                            ])
df2a
```

--------------------------------

### Get All Clinical Data for a Study

Source: https://pybioportal.readthedocs.io/en/latest/clinical_data.html

Retrieves all clinical data associated with a given study ID. This is useful for a comprehensive overview of the clinical attributes within a study.

```python
df1 = cd.get_all_clinical_data_of_study(study_id="brca_tcga")
df1
```

--------------------------------

### Fetch Generic Assay Data Across Multiple Molecular Profiles

Source: https://pybioportal.readthedocs.io/en/latest/generic_assay_data.html

Fetches generic assay data for specified assay IDs across multiple molecular profiles. This is useful for comparative analysis across different datasets.

```python
df2a = gad.fetch_generic_assay_data(generic_assay_stable_ids=["TULP4_pS563", "TEP1_pS397", "ALAD_214_215_1_1_S215"],
                                    molecular_profile_ids=["brca_tcga_phosphoprotein_quantification","brain_cptac_2020_phosphoprotein"])
df2a
```

--------------------------------

### Get Patient in Study

Source: https://pybioportal.readthedocs.io/en/latest/patients.html

Retrieves a specific patient's data within a given study. This is useful for accessing detailed information about an individual patient's records.

```python
df4 = pts.get_patient_in_study(patient_id="TCGA-3C-AAAU", study_id="brca_tcga")
df4
```

--------------------------------

### Fetch Generic Assay Metadata by Stable IDs

Source: https://pybioportal.readthedocs.io/en/latest/generic_assays.html

Fetches metadata for generic assays using a list of stable IDs. The output includes stableId, entityType, and associated metadata properties.

```python
df1a = ga.fetch_generic_assay_meta(generic_assay_stable_ids=["TULP4_pS563", "TEP1_pS397", "ALAD_214_215_1_1_S215"])
df1a
```

--------------------------------

### Fetch Sample Clinical Data (Wide Format)

Source: https://pybioportal.readthedocs.io/en/latest/clinical_data.html

Retrieves sample-level clinical data for specified attributes and entities across studies. Returns data in a wide format, where attributes are columns.

```python
df1b = cd.fetch_clinical_data(attribute_ids=["ORGAN_SYSTEM", "SUBTYPE", "CANCER_TYPE", "MUTATION_COUNT"],
                              entity_study_ids=[
                                      {"entity_ids": ["P-0000004-T01-IM3", "P-0000950-T01-IM3"], "study": "msk_met_2021"},
                                      {"entity_ids": ["TCGA-5T-A9QA-01", "TCGA-A1-A0SB-01"], "study": "brca_tcga"}
                              ],
                              clinical_data_type="SAMPLE", ret_format="WIDE")
df1b
```

--------------------------------

### Get Server Status

Source: https://pybioportal.readthedocs.io/en/latest/server_running_status.html

Call the get_server_status() function to retrieve the running status of the server. The function returns a pandas DataFrame indicating the server's operational state.

```python
srs.get_server_status()
```

--------------------------------

### Get Copy Number Segments for a Specific Sample in a Study

Source: https://pybioportal.readthedocs.io/en/latest/copy_number_segment.html

Retrieves copy number segments for a single sample within a specified study. The output is a pandas DataFrame.

```python
df2 = cns.get_copy_number_segments_in_sample_in_study(study_id="msk_met_2021", sample_id="P-0000950-T01-IM3")
df2.head(10)
```

--------------------------------

### Get All Cancer Types

Source: https://pybioportal.readthedocs.io/en/latest/cancer_types.html

Retrieves a DataFrame containing a summary of all cancer types available in cBioPortal. This function is useful for exploring the available cancer types and their basic properties.

```python
df1 = ct.get_all_cancer_types()
df1
```

--------------------------------

### Fetch Mutations in Molecular Profile for Multiple Genes and Samples

Source: https://pybioportal.readthedocs.io/en/latest/mutations.html

Fetch mutations from a specified molecular profile for a list of Entrez gene IDs and a list of sample IDs. This is useful for comparative mutation analysis across different genes and samples.

```python
df2a = mts.fetch_muts_in_mol_prof(molecular_profile_id="brca_tcga_mutations",
                                  entrez_gene_ids=["1005", "1020"],
                                  sample_ids = ["TCGA-AR-A1AR-01","TCGA-BH-A1EO-01"])
df2a
```

--------------------------------

### Import Generic Assays Module

Source: https://pybioportal.readthedocs.io/en/latest/generic_assays.html

Imports the generic_assays module from the pybioportal library.

```python
from pybioportal import generic_assays as ga
```

--------------------------------

### pybioportal.samples.fetch_samples

Source: https://pybioportal.readthedocs.io/en/latest/samples.html

Fetches samples based on provided identifiers, sample list IDs, or unique sample keys. Allows specifying the projection for the level of detail in the returned data.

```APIDOC
## fetch_samples

### Description
Fetches samples by ID, sample list IDs, or unique sample keys. Allows specifying the projection for the level of detail in the returned data.

### Method
`pybioportal.samples.fetch_samples`

### Parameters
#### Path Parameters
None

#### Query Parameters
* **sample_identifiers** (list of dict) - Required - List of Sample ID / Study ID pairs. Each dict should have the following format: `[{'sample_ids': ['TCGA-AR-A1AR-01', ...], 'study_id': 'brca_tcga'}, ...]`
* **sample_list_ids** (list of str) - Optional - List of Sample List IDs (e.g., `['brca_tcga_cna', 'brca_tcga_mrna', 'brca_tcga_pub_cna']`).
* **unique_sample_keys** (list of str) - Optional - List of Unique Sample Keys, e.g. `['VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ', ...]`
* **projection** (str) - Optional - Level of detail of the response. Possible values: `"DETAILED"`, `"ID"`, `"META"`, `"SUMMARY"` (default).

### Request Example
```python
# Example for sample_identifiers
samples = pybioportal.samples.fetch_samples(
    sample_identifiers=[
        {"sample_ids": ["TCGA-AR-A1AR-01", "TCGA-BH-A1EO-01", "TCGA-BH-A1ES-01"],
         "study_id": "brca_tcga"},
        {"sample_ids": ["TCGA-A2-A0T2-01", "TCGA-A2-A04P-01"],
         "study_id": "brca_tcga_pub"}
    ]
)

# Example for sample_list_ids
samples = pybioportal.samples.fetch_samples(
    sample_list_ids=["brca_tcga_cna", "brca_tcga_mrna"]
)

# Example for unique_sample_keys
samples = pybioportal.samples.fetch_samples(
    unique_sample_keys=["VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ", ...]
)
```

### Response
#### Success Response (200)
Returns a pandas.DataFrame containing samples by ID.

#### Response Example
```
# DataFrame structure depends on the projection used.
# Example for SUMMARY projection:
#      SAMPLE_ID  PATIENT_ID   STUDY_ID
# 0  TCGA-AR-A1AR-01  TCGA-AR-A1AR  brca_tcga
# 1  TCGA-BH-A1EO-01  TCGA-BH-A1EO  brca_tcga
```
```

--------------------------------

### Fetch Molecular Profiles by IDs

Source: https://pybioportal.readthedocs.io/en/latest/molecular_profiles.html

Retrieve molecular profiles by specifying a list of molecular profile IDs. Displays the entire resulting DataFrame.

```python
df3a = mf.fetch_molecular_profiles(molecular_profile_ids=["brca_tcga_mrna", "acc_tcga_rna_seq_v2_mrna"])
df3a
```

--------------------------------

### pybioportal.sample_lists.fetch_sample_lists

Source: https://pybioportal.readthedocs.io/en/latest/sample_lists.html

Fetches sample lists by their IDs with a specified projection level.

```APIDOC
## fetch_sample_lists

### Description
Fetches sample lists by ID. Allows specifying the level of detail for the returned information.

### Method
Not applicable (Python function)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **sample_list_ids** (_list of str_) – Required - List of sample list IDs.
* **projection** (_str_) – Optional - Level of detail of the response. Possible values: "DETAILED", "ID", "META", "SUMMARY" (default).

### Returns
A DataFrame containing sample lists.

### Return Type
pandas.DataFrame
```

--------------------------------

### Import pybioportal gene_panel_data module

Source: https://pybioportal.readthedocs.io/en/latest/gene_panel_data.html

Imports the necessary module for fetching gene panel data.

```python
from pybioportal import gene_panel_data as gpd
```

--------------------------------

### Get a specific clinical attribute in a study

Source: https://pybioportal.readthedocs.io/en/latest/clinical_attributes.html

Retrieve a single, specific clinical attribute for a given study ID and clinical attribute ID. Useful for targeted data retrieval.

```python
df4 = ca.get_clinical_attribute_in_study(study_id="brca_tcga", clinical_attribute_id="AGE")
df4
```

--------------------------------

### Fetch gene panel data by molecular profile IDs

Source: https://pybioportal.readthedocs.io/en/latest/gene_panel_data.html

Fetches gene panel data for a list of specified molecular profile IDs. The output includes sample and patient information.

```python
df1a = gpd.fetch_gene_panel_data(molecular_profile_ids=["brca_tcga_gistic", "acc_tcga_gistic", "brca_tcga_mutations"])
df1a
```

--------------------------------

### Get a specific gene panel by ID

Source: https://pybioportal.readthedocs.io/en/latest/gene_panels.html

Fetch a gene panel using its unique identifier. Use `.head(10)` to display the first 10 rows of the resulting DataFrame.

```python
df2 = gp.get_gene_panel("NSCLC_UNITO_2016_PANEL")
df2.head(10)
```

--------------------------------

### Get All Clinical Data for a Specific Patient

Source: https://pybioportal.readthedocs.io/en/latest/clinical_data.html

Retrieves all available clinical data for a single patient within a given study. This provides a detailed view of a patient's clinical information.

```python
df4 = cd.get_all_clinical_data_of_patient_in_study(study_id="brca_tcga", patient_id="TCGA-5T-A9QA")
df4
```

--------------------------------

### Fetch Molecular Profiles by Study IDs

Source: https://pybioportal.readthedocs.io/en/latest/molecular_profiles.html

Retrieve molecular profiles by specifying a list of study IDs. Displays the first 5 rows of the resulting DataFrame.

```python
df3b = mf.fetch_molecular_profiles(study_ids=["brca_tcga", "acc_tcga"])
df3b.head(5)
```

--------------------------------

### Import PyBioPortal Mutations Module

Source: https://pybioportal.readthedocs.io/en/latest/mutations.html

Import the necessary mutations module from the PyBioPortal library.

```python
from pybioportal import mutations as mts
```

--------------------------------

### Import Molecular Profiles Module

Source: https://pybioportal.readthedocs.io/en/latest/molecular_profiles.html

Import the molecular_profiles module from the pybioportal library.

```python
from pybioportal import molecular_profiles as mf
```

--------------------------------

### Get Aliases of a Gene

Source: https://pybioportal.readthedocs.io/en/latest/genes.html

Retrieve all known aliases for a given gene, identified by its Hugo Gene Symbol or Entrez Gene ID. This is useful for discovering alternative names a gene might be known by.

```python
df3 = gns.get_aliases_of_gene("BRCA2")
df3
```

--------------------------------

### Import pybioportal gene_panels module

Source: https://pybioportal.readthedocs.io/en/latest/gene_panels.html

Import the necessary module for gene panel operations.

```python
from pybioportal import gene_panels as gp
```

--------------------------------

### Fetch Generic Assay Data

Source: https://pybioportal.readthedocs.io/en/latest/generic_assay_data.html

Fetches generic assay data from multiple molecular profiles. Can filter by assay IDs, molecular profile IDs, or sample-molecular identifier pairs. Use 'SUMMARY' projection for default detail level.

```python
pybioportal.generic_assay_data.fetch_generic_assay_data(_generic_assay_stable_ids =None_, _molecular_profile_ids =None_, _sample_molecular_identifiers =None_, _projection ='SUMMARY'_)
```

--------------------------------

### Fetch Generic Assay Metadata by Molecular Profile IDs

Source: https://pybioportal.readthedocs.io/en/latest/generic_assays.html

Fetches metadata for generic assays associated with specific molecular profile IDs. The results contain stableId, entityType, and gene symbol/phosphosite information.

```python
df1b = ga.fetch_generic_assay_meta(molecular_profile_ids=["brca_tcga_phosphoprotein_quantification",
                                                          "brain_cptac_2020_phosphoprotein"])
df1b
```

--------------------------------

### Treatments

Source: https://pybioportal.readthedocs.io/en/latest/modules.html

Functions for fetching treatment data at patient and sample levels.

```APIDOC
## fetch_all_patient_level_treatments()

### Description
Fetches all patient-level treatment data.

### Method
POST

### Endpoint
/patient_level_treatments/fetch

## fetch_all_sample_level_treatments()

### Description
Fetches all sample-level treatment data.

### Method
POST

### Endpoint
/sample_level_treatments/fetch

## fetch_status_display_patient_trts()

### Description
Fetches patient treatments for status display.

### Method
POST

### Endpoint
/patient_treatments/status_display/fetch

## fetch_status_display_sample_trts()

### Description
Fetches sample treatments for status display.

### Method
POST

### Endpoint
/sample_treatments/status_display/fetch
```