This function returns a list of all available compendia in refine.bio.
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
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.
See also
Other refine.bio API:
rb_entity_list(),
rb_institution_list(),
rb_organism_list(),
rb_platform_list()
Author
Sean Davis seandavi@gmail.com
Examples
# note that the download links are specific to my account
# and will not work for you.
compendia <- rb_compendia_list()
colnames(compendia)
#> [1] "id" "primary_organism_name" "organism_names"
#> [4] "svd_algorithm" "quant_sf_only" "compendium_version"
#> [7] "computed_file"
head(compendia)
#> id primary_organism_name organism_names svd_algorithm quant_sf_only
#> 1 589 ACTINIDIA_CHINENSIS NONE TRUE
#> 2 109 ACTINIDIA_CHINENSIS ACTINIDI.... NONE TRUE
#> 3 46 ACYRTHOSIPHON_PISUM ACYRTHOS.... NONE TRUE
#> 4 531 ACYRTHOSIPHON_PISUM NONE TRUE
#> 5 136 AEDES_AEGYPTI AEDES_AE.... NONE TRUE
#> 6 612 AEDES_AEGYPTI NONE TRUE
#> compendium_version computed_file.id computed_file.filename
#> 1 2 5835775 ACTINIDIA_CHINENSIS_rnaseq_compendia.zip
#> 2 1 5741249 ACTINIDIA_CHINENSIS_rnaseq_compendia.zip
#> 3 1 5741187 ACYRTHOSIPHON_PISUM_rnaseq_compendia.zip
#> 4 3 5835614 ACYRTHOSIPHON_PISUM_rnaseq_compendia.zip
#> 5 1 5741270 AEDES_AEGYPTI_rnaseq_compendia.zip
#> 6 2 5835836 AEDES_AEGYPTI_rnaseq_compendia.zip
#> computed_file.size_in_bytes computed_file.is_smashable computed_file.is_qc
#> 1 7712841 FALSE FALSE
#> 2 7712716 FALSE FALSE
#> 3 113243373 FALSE FALSE
#> 4 113245027 FALSE FALSE
#> 5 188123029 FALSE FALSE
#> 6 287220543 FALSE FALSE
#> computed_file.sha1
#> 1 57ed61590a46d5a088c14264335e6882d7847666
#> 2 04e91e874ecf410287f3f932faef501930639ba1
#> 3 887f2459b8d4605087f312af8a59f9ef45aaf182
#> 4 7885162bcf4067eeaeff5caeb94f3645b53bb90d
#> 5 4306f65b3c487b227214b5027b50392958534d98
#> 6 179cc254b7bd82a1af0c245038a19214a2083187
#> computed_file.s3_bucket computed_file.s3_key
#> 1 data-refinery-s3-compendia-circleci-prod ACTINIDIA_CHINENSIS_2_1601573377.zip
#> 2 data-refinery-s3-compendia-circleci-prod ACTINIDIA_CHINENSIS_1_1574120893.zip
#> 3 data-refinery-s3-compendia-circleci-prod ACYRTHOSIPHON_PISUM_1_1574119636.zip
#> 4 data-refinery-s3-compendia-circleci-prod ACYRTHOSIPHON_PISUM_3_1601571720.zip
#> 5 data-refinery-s3-compendia-circleci-prod AEDES_AEGYPTI_1_1574121066.zip
#> 6 data-refinery-s3-compendia-circleci-prod AEDES_AEGYPTI_2_1601573868.zip
#> computed_file.download_url
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#> 6 2020-10-01T17:37:48.037411Z 2020-10-01T17:37:49.980029Z