get_compendia_catalog: All available compendia in refine.bio

In seandavi/RefineBio: The bridge between refine.bio and Bioconductor

All available compendia in refine.bio

Description

This function returns a list of all available compendia in refine.bio.

Usage

get_compendia_catalog()

Details

We periodically release compendia comprised of all the samples from a species that we were able to process. We refer to these as refine.bio compendia. We offer two kinds of refine.bio compendia:count

• Normalized compendia

• RNA-seq compendia

Both types of compendia are available for download from the RefineBio website. The details of how these compendia are generated are described in the RefineBio site documentation and summarized here for convenience.

Normalized compendia

Refine.bio normalized compendia are comprised of all the samples from a species that we were able to process, aggregate, and normalize. Normalized compendia provide a snapshot of the most complete collection of gene expression that refine.bio can produce for each supported organism. They process these compendia in a manner that is different from the options that are available via the web user interface. Note that submitter processed samples that are available through the web user interface are omitted from normalized compendia because these samples can introduce unwanted technical variation.

The refine.bio web interface does an inner join when datasets are combined, so only genes present in all datasets are included in the final matrix. For compendia, they take the union of all genes, filling in any missing values with NA. This is a “full outer join” as illustrated in the RefineBio site documentation. They use a full outer join because it allows us to retain more genes in a compendium and then impute missing values during compendia creation.

RNA-seq sample compendia

refine.bio RNA-seq sample compendia are comprised of the Salmon output for the collection of RNA-seq samples from an organism that we have processed with refine.bio. Each individual sample has its own quant.sf file; the samples have not been aggregated and normalized. RNA-seq sample compendia are designed to allow users that are comfortable handling these files to generate output that is most useful for their downstream applications. Please see the Salmon documentation on the quant.sf output format for more information.

Downloading compendia

Both types of compendia are available for download. The download links are listed in the computed_file.download_url field of the results of this query. You can use the download.file function in R to download the compendia that you are interested in.

Value

data.frame The results of the query.

Author(s)

Sean Davis [e-mail]

Examples

# note that the download links are specific to my account
# and will not work for you.
compendia <- get_compendia_catalog()

colnames(compendia)

head(compendia)

## Not run: 
td <- tempdir()
download.file(
  compendia$computed_file.download_url[1],
  destfile = file.path(td, "compendium.zip")
)
list.files(td)

## End(Not run)

seandavi/RefineBio documentation built on June 1, 2025, 4:10 p.m.