genesbyringqvistfoldchange: Find genes that are differentially expressed based on growth...

In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description

Find genes that are differentially expressed based on growth conditions. Select a comparison and reference growth conditions, your desired fold induction and the direction of regulation. <BR>Interaction experiments were performed between G. intestinalis GL50803 and 21-day differentiated Caco-2 cells. Trophozoites were separated and collected from the interaction cultures at 1.5 h, 6 h and 18 h time points. In addition, trophozoites of the same time points were harvested from standard TYI-S-33 cultures and from cultures in only interaction medium (DMEM). Microarrays of all samples and time points were performed with a common reference, a pool of trophozoites from the 0 hr time point of three replicate experiments. At least two 2-channel arrays were performed for each time point.

Arguments

ringqvist_reference	Select a growth condition.
ringqvist_comparitor	Select a growth condition.
fold_change	Enter a non-negative number. NOTE: Fold change is reported in the summary as positive numbers for up-regulated genes and negative numbers for down-regulated genes
regulated_dir	For ConditionA vs. ConditionB, select up-regulated for genes where ConditionA > ConditionB and select down-regulated for genes where ConditionB > ConditionA.
protein_coding_only	Should only protein coding genes be returned?
o-fields	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
o-tables	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
.convert	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and TRUE, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is FALSE, the value from the Web server is returned as is.
.url	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
.json	a logical value controlling whether to use the JSON or the XML version of the method

Value

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duncantl/REuPathDB documentation built on May 15, 2019, 5:28 p.m.