Analysis Service¶

Pathway Analysis Service Provides pathway over-representation and expression analysis as well as species comparison tool

API calls are avaialble @ https://reactome.org/AnalysisService/#/

Data model key classes for id query are available @ https://reactome.org/documentation/data-model

reactome2py.analysis.compare_species(species='48892', page_size='1', page='1', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL', p_value='1')¶

Compares Homo sapiens to the specified species

Parameters

species -- The reactome dbId string of the species to compare to ex. of some dbId mappings {'Homo sapiens':'48887', 'Mus musculus':'48892', 'Rattus norvegicus':'48895', 'Sus scrofa':'49633', 'Xenopus tropicalis':'205621', 'Bos taurus':'48898', 'Gallus gallus':'49591'}
page_size -- Page size
page -- Number of pages
sort_by -- How to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- Order ASC or DESC
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned

Returns

Json dictionary object

reactome2py.analysis.db_name()¶

The name of current database

Returns: String of the name of current database.

reactome2py.analysis.db_version()¶

The version number of current database

Returns: String of the version number of current database.

reactome2py.analysis.found_entities(token, path='', resource='TOTAL', file='result.csv', save=False, chunk_size=128)¶

list of found entities in reactome database

Parameters

token -- The token associated with the data result - analysis Web-Service is token based so for every analysis request a TOKEN is associated to the result
path -- Absolute path to save the csv file to
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
file -- File name default is set to result.csv
save -- If true saves the result data frame as csv file, else it returns the data frame
chunk_size -- Python generator iter_content() chunk size - default set to 128

Returns

Pandas data frame with genes or entities found in pathway enrichment analysis overlap

reactome2py.analysis.identifier(id='EGFR', interactors=False, page_size='1', page='1', species='Homo Sapiens', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None, projection=False)¶

Given a protein, gene, or small molecule identifier symbol conducts analysis of the identifier over different species and pathways in reactome database.

Parameters

id -- A protein, gene or small molecule identifier symbol id ex. EGFR
interactors -- Boolean value if set to false, your query will consider only manually curated Reactome pathways with known biological significance. if true, your query will consider Reactome pathways that have been expanded by including all available protein-protein interactors from the IntAct database
page_size -- Page size
page -- Number of pages
species -- List of species to filter the result (accepts taxonomy ids, species names and reactome dbId)
sort_by -- How to sort the result. Available filters TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- Order ASC or DESC
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
projection -- If true, projects the identifiers to human and only shows the result in this species
max_entities -- Maximum number of contained entities per pathway (takes into account the resource)
min_entities -- Minimum number of contained entities per pathway (takes into account the resource)

Returns

Json dictionary object

reactome2py.analysis.identifiers(ids='EGF,EGFR', interactors=False, page_size='1', page='1', species='Homo Sapiens', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None, projection=False)¶

Given a list of protein, gene, or small molecule identifiers conducts reactome pathway enrichment analysis.

Parameters

ids -- comma seperated list of proteins, genes or small molecules identifiers symbol in string format ex. 'EGF,EGFR'
interactors -- boolean value indicating include interations
page_size -- page size
page -- number of pages
species -- list of species to filter the result (accepts taxonomy ids, species names and dbId)
sort_by -- how to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- order ASC or DESC
resource -- the resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
projection -- if true, projects the identifiers to human and only shows the result in this species
max_entities -- maximum number of contained entities per pathway (takes into account the resource)
min_entities -- minimum number of contained entities per pathway (takes into account the resource)

Returns

Json dictionary object

reactome2py.analysis.identifiers_form(path, interactors=False, page_size='1', page='1', species='Homo Sapiens', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None, projection=False)¶

Given a file path with a list of identifiers conducts reactome pathway enrichment analysis

Parameters

path -- absolute path to the the txt file with identifier symbols to be analysed - refer to https://reactome.org/dev/analysis for format.
interactors -- boolean value if set to false, your query will consider only manually curated Reactome pathways with known biological significance. if true, your query will consider Reactome pathways that have been expanded by including all available protein-protein interactors from the IntAct database.
page_size -- page size
page -- number of pages
species -- list of species to filter the result (accepts taxonomy ids, species names and dbId)
sort_by -- how to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- order ASC or DESC
resource -- the resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
projection -- if true, projects the identifiers to human and only shows the result in this species
max_entities -- maximum number of contained entities per pathway (takes into account the resource)
min_entities -- minimum number of contained entities per pathway (takes into account the resource)

Returns

reactome2py.analysis.identifiers_mapping(ids='EGF,EGFR', interactors=False, projection=False)¶

Maps the identifiers passed as a comma seperated list in str format over the different species and if projection is set to true, projects the result to Homo Sapiens

Parameters

ids -- Comma seperated list of proteins, genes or small molecules identifiers symbol in string format ex. 'EGF,EGFR'
interactors -- boolean value if set to false, your query will consider only manually curated Reactome pathways with known biological significance. if true, your query will consider Reactome pathways that have been expanded by including all available protein-protein interactors from the IntAct database.
projection -- If true, projects the identifiers to human and only shows the result in this species

Returns

Json list object

reactome2py.analysis.identifiers_mapping_form(path, interactors=False, projection=False)¶

Maps the identifiers passed via txt file over the different species and if projection is set to true, projects the result to Homo Sapiens

Parameters

path -- Absolute path to the the txt file with identifier symbols to be analysed - refer to https://reactome.org/dev/analysis for format.
interactors -- boolean value if set to false, your query will consider only manually curated Reactome pathways with known biological significance. if true, your query will consider Reactome pathways that have been expanded by including all available protein-protein interactors from the IntAct database.
projection -- If true, projects the identifiers to human and only shows the result in this species

Returns

reactome2py.analysis.identifiers_mapping_url(external_url, interactors=False, projection=False)¶

Maps the identifiers passed via url over the different species and if projection is set to true, projects the result to Homo Sapiens

Parameters

external_url --
interactors -- Boolean value if set to false, your query will consider only manually curated Reactome pathways with known biological significance. if true, your query will consider Reactome pathways that have been expanded by including all available protein-protein interactors from the IntAct database.
projection -- If true, projects the identifiers to human and only shows the result in this species

Returns

reactome2py.analysis.identifiers_url(external_url, interactors=False, page_size='1', page='1', species='Homo Sapiens', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None, projection=False)¶

Given a url with a list of identifiers conducts reactome pathway enrichment analysis

Parameters

external_url -- Url containing identifiers id symbols
interactors -- Boolean value if set to false, your query will consider only manually curated Reactome pathways with known biological significance. if true, your query will consider Reactome pathways that have been expanded by including all available protein-protein interactors from the IntAct database.
page_size -- Page size
page -- Number of pages
species -- List of species to filter the result (accepts taxonomy ids, species names and dbId)
sort_by -- How to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- Order ASC or DESC
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
projection -- If true, projects the identifiers to human and only shows the result in this species
max_entities -- Maximum number of contained entities per pathway (takes into account the resource)
min_entities -- Minimum number of contained entities per pathway (takes into account the resource)

Returns

reactome2py.analysis.import_form(input_file)¶

Imports the posted json file into the service The accepted format is the same as provided by the method /#/download/{token}/result.json. Note: The submitted file can be gzipped.

Parameters: input_file -- A json file with the data to be analysed
Returns

reactome2py.analysis.import_json(input_json)¶

Imports the posted json into the service The accepted format is the same as provided by the method /#/download/{token}/result.json. Note: The provided file can be gzipped.

Parameters: input_json -- Identifiers to analyse followed by their expression (when applies) in json format in string
Returns

reactome2py.analysis.import_url(input_url)¶

Imports the json file provided by the posted url into the service The accepted format is the same as provided by the method /#/download/{token}/result.json. Note: The provided file can be gzipped.

Parameters: input_url -- A URL pointing to the json data to be analysed
Returns

reactome2py.analysis.pathway2df(token, path='', resource='TOTAL', file='result.csv', save=False, chunk_size=128)¶

Create a Data frame of the analysis result for all the pathway hits - save to csv file (comma separated)

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
path -- Absolute path to save the file containing analysis results to
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
file -- File name to save the analysis results to
save -- Boolean value if true - saves data frame as csv file. default is set to false.
chunk_size -- Python generator iter_content() chunk size - default set to 128

Returns

Saves the result as csv file or returns a pandas data frame

reactome2py.analysis.report(token, path, file='report.pdf', number='25', resource='TOTAL', diagram_profile='Modern', analysis_profile='Standard', fireworks_profile='Barium Lithium', species='Homo sapiens', chunk_size=128)¶

Downloads a report for a given pathway analysis result

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
path -- Absolute path to save the report pdf file to
file -- Pdf file name to save the analysis report to - default set to report.pdf
number -- Number of pathways reported (max 50)
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
diagram_profile -- Diagram Color Profile - as string
analysis_profile -- Analysis Color Profile - as string
fireworks_profile -- Diagram Color Profile - as string
species -- The species for which results will be reported
chunk_size -- Python generator iter_content() chunk size - default set to 128

Returns

Saves a reactome analysis pdf report to the indicated path and file name

reactome2py.analysis.result2json(token, path='', file='result.json', save=False, gzip=False, chunk_size=128)¶

View of analysis result in json format

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
path -- Absolute path to save the file containing analysis results to
file -- File name to save the analysis results to
save -- Boolean value if true - saves result as json file. default is set to false.
gzip -- Boolean value if true - saves result as gzipped json file. default is set to false.
chunk_size -- Python generator iter_content() chunk size - default set to 128

Returns

File or json object containing data on pathway, entities, statistics, etc. found in analysis overlap

reactome2py.analysis.token(token, species='Homo sapiens', page_size='1', page='1', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None)¶

Returns the result associated with token. Use page and pageSize to reduce the amount of data retrieved. Use sortBy and order to sort the result by your preferred option. The resource field will filter the results to show only those corresponding to the preferred molecule type (TOTAL includes all the different molecules type)

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
species -- List of species to filter the result (accepts taxonomy ids, species names and reactome dbId)
page_size -- Page size
page -- Page number
sort_by -- How to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- Order ASC or DESC
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
min_entities -- Minimum number of contained entities per pathway (takes into account the resource)
max_entities -- Maximum number of contained entities per pathway (takes into account the resource)

Returns

Json dictionary object

reactome2py.analysis.token_filter_species(token, species='Homo sapiens', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL')¶

Queries analysis token and returns and filters the result by species

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
species -- List of species to filter the result (accepts taxonomy ids, species names and reactome dbId)
sort_by -- How to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- Order ASC or DESC
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND

Returns

Json dictionary object

reactome2py.analysis.token_pathway_page(token, pathway, page_size='1', sort_by='ENTITIES_FDR', order='ASC', resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None)¶

Returns the page where the corresponding pathway is taking into account the passed parameters

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
pathway -- The pathway stable identifier (stId - provided in the analysis result for each pathway)
page_size -- Page size
sort_by -- How to sort the result. Available filters: TOTAL_ENTITIES, TOTAL_REACTIONS, TOTAL_INTERACTIONS, FOUND_ENTITIES, FOUND_INTERACTIONS, FOUND_REACTIONS, ENTITIES_RATIO, ENTITIES_PVALUE, ENTITIES_FDR, REACTIONS_RATIO
order -- Order ASC or DESC
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
min_entities -- Minimum number of contained entities per pathway (takes into account the resource)
max_entities -- Maximum number of contained entities per pathway (takes into account the resource)

Returns

int

reactome2py.analysis.token_pathway_reactions(token, pathway, resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None)¶

Returns the reaction ids a or one pathway's stable identifiers (stId) that is present in the original result

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
pathway -- The pathway stable identifier (stId - provided in the analysis result for each pathway)
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
min_entities -- Minimum number of contained entities per pathway (takes into account the resource)
max_entities -- Maximum number of contained entities per pathway (takes into account the resource)

Returns

list

reactome2py.analysis.token_pathway_summary(token, pathway, resource='TOTAL', page='1', page_size='1', by='all')¶

Queries analysis token and returns a summary of

by='all': all the contained identifiers and interactors
by='entities': the found curated identifiers
by='interactors': the found interactors (may return null or none)

for a given pathway and token

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
pathway -- The pathway stable identifier (stId - provided in the analysis result for each pathway)
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
page -- Page number
page_size -- Page size
by -- Filter found cases by: all, entities, interactors

Returns

Json dictionary object

reactome2py.analysis.token_pathways_binned(token, resource='TOTAL', bin_size='100', p_value='1', include_disease=True)¶

Returns a list of binned hit pathway sizes associated with the token

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
bin_size -- Defines the size of each bin for the classification (min: 100)
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)

Returns

Json list object

reactome2py.analysis.token_pathways_reactions(token, pathways, resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None)¶

Returns the reaction ids of all the pathway stable identifiers (stIds) that are present in the original result

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
pathways -- The pathways stable identifier (stId - provided in the analysis result for each pathway)
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
min_entities -- Minimum number of contained entities per pathway (takes into account the resource)
max_entities -- Maximum number of contained entities per pathway (takes into account the resource)

Returns

list

reactome2py.analysis.token_pathways_result(token, pathways, species='Homo sapiens', resource='TOTAL', p_value='1', include_disease=True, min_entities=None, max_entities=None)¶

For a given list of pathway stable identifiers (stId) it will query and retrieve a list containing those that are present in the result (with the results for the indicated molecule type)

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
pathways -- The pathways stable identifiers (stId - provided in the analysis result for each pathway)
species -- List of species to filter the result (accepts taxonomy ids, species names and reactome dbId)
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND
p_value -- Defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
include_disease -- Set to ‘false’ to exclude the disease pathways from the result (it does not alter the statistics)
min_entities -- Minimum number of contained entities per pathway (takes into account the resource)
max_entities -- Maximum number of contained entities per pathway (takes into account the resource)

Returns

Json list object

reactome2py.analysis.token_pathways_summary(token, pathways, resource='TOTAL')¶

Queries analysis token and returns a summary of the contained identifiers and interactors for all pathways

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
pathways -- The pathways stable identifier (stId - provided in the analysis result for each pathway)
resource -- The resource to sort TOTAL, UNIPORT, ENSEMBLE, CHEMBI, IUPHAR, MIRBASE, NCBI_PROTEIN, EMBL, COMPOUND, PUBCEM_COMPOUND

Returns

Json list object

reactome2py.analysis.token_resources(token)¶

the resources summary associated with the token

Parameters: token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
Returns: Json list object

reactome2py.analysis.token_unfound_identifiers(token, page_size='1', page='1')¶

Returns a list of the identifiers not found for a given token

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
page_size -- Page size
page -- Number of pages

Returns

list

reactome2py.analysis.unfound_entities(token, path='', file='result.csv', save=False, chunk_size=128)¶

list of unfound entities in reactome database

Parameters

token -- The token associated with the data result - analysis Web-Service is token based, so for every analysis request a TOKEN is associated to the result
file -- File name default is set to result.csv
path -- Absolute path to save the csv file to
save -- If true saves the result data frame as csv file, else it returns the data frame
chunk_size -- Python generator iter_content() chunk size - default set to 128

Returns

Pandas data frame with genes or entities not found in pathway enrichment analysis overlap

Analysis Service¶

reactome2py

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