## ----eval=FALSE----------------------------------------------------------
# library(geneXplainR)
# # Words within placeholders (<...>) need to be replaced.
# gx.login("<server>","<user>","<password>")
## ----eval=FALSE----------------------------------------------------------
# gx.logout()
## ----eval=FALSE----------------------------------------------------------
# #... after login
# # Get the list of available tools
# gx.analysis.list()
#
# # Show parameters for a specific tool
# gx.analysis.parameters("Convert table")
#
# # Invoke an analysis with the tool
# gx.analysis("Convert table", list(sourceTable = "data/Projects/Example/Data/example_table",
# species = "Human (Homo sapiens)",
# sourceType = "Genes: Ensembl",
# targetType = "Genes: Gene symbol",
# outputTable = "data/Projects/Example/Data/example_output_table"))
## ----eval=FALSE----------------------------------------------------------
# #... after login
# # Get list of workflows in 'Common'
# gx.ls("analyses/Workflows/Common")
#
# # Get parameters for specific workflow
# gx.ls("analyses/Workflows/Common/Gene set enrichment analysis (Gene table)")
#
# # Invoke workflow
# gx.workflow("analyses/Workflows/Common/Gene set enrichment analysis (Gene table)",
# list("Input table" = "data/Projects/Example/Data/example_table",
# "Enrichment Weight Column" = "Column name",
# "Species" = "Mouse (Mus musculus)",
# "Results folder" = "data/Projects/Example/Data/example_output"))
## ------------------------------------------------------------------------
library(geneXplainR)
?gx.vennDiagrams
## ----eval=FALSE----------------------------------------------------------
# #... after login
# # Words in placeholders (<...>) need to be replaced with suitable values.
# gx.put("data/Projects/<project name>/Data/<destination folder>", data)
# data <- gx.get("data/Projects/<project name>/Data/<source folder>/<platform table>")
## ----eval=FALSE----------------------------------------------------------
# #... after login
# # Words in placeholders (<...>) need to be replaced with suitable values.
# gx.importers()
# gx.import.parameters("data/Projects/<project name>/Data/<destination folder>", "<importer name>")
# gx.import("<local file>", "<platform destination path>", "<importer>", list("<parameter>"="<value>"))
## ----eval=FALSE----------------------------------------------------------
# #... after login
# # Words in placeholders (<...>) need to be replaced with suitable values.
# gx.exporters()
# gx.export.parameters("data/Projects/<project name>/Data/<item to export>", "<exporter name>")
# gx.export("<platform item>", "<exporter>", list("<parameter>"="<value>"), "local file")
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