advanced_search_by_genes
(Package: Rcolombos) :
Accessory function allowing the advanced_search by gene_ids, go, annotation
Accessory function allowing the advanced_search by gene_ids, go, annotation
● Data Source:
CranContrib
● Keywords:
● Alias: advanced_search_by_genes
●
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listContrasts
(Package: Rcolombos) :
This method takes as parameter a single string, representing an organism,
This method takes as parameter a single string, representing an organism, and returns a character vector corresponding to the currently available organisms.
● Data Source:
CranContrib
● Keywords:
● Alias: listContrasts
●
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listGenes
(Package: Rcolombos) :
This method takes as parameter a single string, representing an organism,
This method takes as parameter a single string, representing an organism, and returns a character vector corresponding to the currently available organisms.
● Data Source:
CranContrib
● Keywords:
● Alias: listGenes
●
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listEntities
(Package: Rcolombos) :
This method takes a string containing the nickname for the selected organism and a string containing the annotation type
This method takes a string containing the nickname for the selected organism and a string containing the annotation type and return the available entities
● Data Source:
CranContrib
● Keywords:
● Alias: listEntities
●
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switchVersion
(Package: Rcolombos) :
Select the COLOMBOS REST API version to be used for retrieving data
Select the COLOMBOS REST API version to be used for retrieving data
● Data Source:
CranContrib
● Keywords:
● Alias: switchVersion
●
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Rcolombos
(Package: Rcolombos) :
Interface to Colombos Compendia using the Exposed REST API
Provides programmatic access to Colombos, a web based interface for exploring and analyzing comprehensive organism-specific cross-platform expression compendia of bacterial organisms.
● Data Source:
CranContrib
● Keywords:
● Alias: Rcolombos, Rcolombos-package
●
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listAnnotationTypes
(Package: Rcolombos) :
This method takes as parameter a string (the nickname of an organism) and returns a character vector
This method takes as parameter a string (the nickname of an organism) and returns a character vector corresponding to the currently available annotation type for the selected organism.
● Data Source:
CranContrib
● Keywords:
● Alias: listAnnotationTypes
●
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quick_search
(Package: Rcolombos) :
This method mimics the quick_search functionality of Colombos.
This method mimics the quick_search functionality of Colombos. It takes a string containg the nickname for the selected organism and a vector of string representing the genes of interest for the specified organism and returns a list containing the locustags (gene_names), contrasts and M-values for the current selection.
● Data Source:
CranContrib
● Keywords:
● Alias: quick_search
●
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get_contrast_annotations
(Package: Rcolombos) :
This method allows to retrieve all the annotations for the Reference and Test conditions for a selected organism (nickname) and for a user specified contrast name. Please be aware that only one contrast is allowed in input. It returns a list containing both ReferenceAnnnotation and TestAnnotation.
This method allows to retrieve all the annotations for the Reference and Test conditions for a selected organism (nickname) and for a user specified contrast name. Please be aware that only one contrast is allowed in input. It returns a list containing both ReferenceAnnnotation and TestAnnotation. and return the available entities
● Data Source:
CranContrib
● Keywords:
● Alias: get_contrast_annotations
●
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advanced_search_by_both
(Package: Rcolombos) :
Accessory function allowing the advanced_search by both g_ids and c_ids
Accessory function allowing the advanced_search by both g_ids and c_ids
● Data Source:
CranContrib
● Keywords:
● Alias: advanced_search_by_both
●
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providing 
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