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HITChip
antagomir edited this page Oct 31, 2014
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Run the following commands in R (on a computer or virtual machine that has access to the database).
You can request the username, password, database name and port from the admins. You also need SSH port forwarding, ask for more instructions.
The program will guide you through preprocessing by asking to specify the projects, samples, and preprocessing parameters. For further instructions, contact the admins.
# First update the HITChipDB package
library(devtools)
install_github(repo = "HITChipDB", username = "microbiome")
# Load the package
library(HITChipDB)
# Run profiling script over FTP
# NOTE: need to ssh port forwarding for localhost first - detailed instructions from the admins!
# NOTE: request the correct dbpwd and port from the admins (see above)
params <- run.profiling.script(dbuser = "root", dbpwd = "array", dbname = "Phyloarray", host = '127.0.0.1', port = ask.correct.port.number.from.admins) This prompts you through profiling options described in full instructions.