The MEMA package includes functions to preprocess, QA, normalize and explore Microenvironment Microarray (MEMA) experiments. MEMAs are used in Oregon Health and Science's (OHSU) MEP-LINCS project. An over veiw of the project along with all data and protocols are avilable at https://www.synapse.org/#!Synapse:syn2862345/wiki/72486.
The functions in this package assume the data is stored on the MEP-LINCS Synapse website or in a relative file structure that mimics the original server structure as described below:
top level directories named by each well plate's barcode value
A subdirectory named "Analysis" an2omero_barcode.tsv contains metadata about the cell lines and reagents in the well plate barcode_level1.tsv contains cell level data and metadata barcode_Lebel2.tsv contains spot level data and metadata
A subdirectory under "Analysis" named by the segmentation pipeline version such as "v2" Raw data files from the segmentation pipeline
a directory named "study"
The functions in this package support data from both CellProfiler and GE InCell segmentation pipelines. The metadata can come OHSU's An! metadata database or excel files. MEMAs can be in 8 or 96 well plates.
devtools::install_github("MEP-LINCS/MEMA")
or the development version with the command:
devtools::install_github("MEP-LINCS/MEMA", ref="develop")
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