MultiAssayExperiment.TCGA
is the pipeline package for building and uploading
MultiAssayExperiment datasets from the GDAC Firehose pipeline as obtained
from RTCGAToolbox
.
There are several steps to rebuild datasets for 33 cancer types.
Generally, users should use the packaged product of the pipeline:
For those looking to rebuild the pipeline, there are several steps that need to be followed:
dataDirectories
)saveRTCGAdata
)ExperimentHub
(buildMultiAssayExperiments
)These functions can be found in the data-raw
, inst/scripts
, and R
folders.
NOTE. Include AWS CLI
authentication credentials in the ~/.Renviron
file.
It should include three key:value pairs,
AWS_SESSION_TOKEN
, AWS_SECRET_ACCESS_KEY
, and AWS_ACCESS_KEY_ID
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