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README.md

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Metadata standardization scripts

Usage

These scripts must be run in the following order:

  1. write_metadata.R This script will pull metadata out of a processed dataset and write the results to a tsv file in $DATA_DIR/metadata. Example: Rscript write_metadata.R arunachalam_2020

  2. standardize_metadata.R This reads in the tsv files generated from write_metadata.R as well as any required supplementary files for each dataset, then merges the results and writes it to $DATA_DIR/metadata/all_meta.tsv.

  3. merge_metadata.R This will merge standard metadata back into the processed h5seurat file, for all datasets. Standard fields get _standard appended to the field name.

  4. add_column_attributes.R This updates the metadata in the h5seurat files with column attributes indicating how they should be displayed in the web portal, for all datasets.

update_metadata.R -- This is a helper script, which will merge updated standardized metadata into the merged dataset.

Supplemental metadata

The files in the supplemental directory are pulled from supplemental files from the publications or provided by authors, and required for deriving standard fields.