Citation

Registration

Linking - (deprecated))

Search Samples (Deprecated)

Previous API Notes (Deprecated)

Genome Coordinates

Gene Lists and Coordinates in Progenetix and arrayMap

For gene coordinates, we use a mapping of the genes’ maximum CDR as derived from mapping resources.

ICD-O 3 Coding

ICD coding of tumor samples

R Integration

Progenetix API and R

With the ability to access the status matrix directly, one easily can import the data into an R data frame:

NCIt Coding

pgx Namespace

Previous API Examples (Deprecated)

Directories and File Structure

The Progenetix Jekyll template modifies the standard Jekyll file structure.

Local Jekyll based website generation

In an ideal scenario, your Github served website could be build locally, with the same output structure and layout.

Format of the YAML Header

The YAML headers are necessary to process the Markdown (or HTML) files in the page collections. The Progenetix Jekyll template uses standard Jekyll headers, but also adds some additional parameters.

Publication Pages

Progenetix segment file format

Publication Pages

The SVGs of the callset heatmap plots will now have labels linked to the sample search script, using the datasetIds and callsets.id parameters. Therefore, one can now easily explore the quality of a callset from the heatmap, w/o having to copy/paste/search.

Beacon Variants in UCSC Browser

The response element of the Beacon+ interface now contains a link for displaying the matched variants e.g. of e.g. a CNV query in the UCSC genome browser.

BeaconPlus in ELIXIR Beacon Network

Progenetix API for Biosamples

After some hiatus we have re-started the work on the Progenetix API. The updated version now has functions for accessing sample data using simple filters.

Examples are e.g. the retrieval of sample data in JSON or tabular format, or the counting of samples matching a given parameter.

Bycon::services.py Python Code Documentation

ByconLibs::beacon_create_handovers.py Python Code Documentation

ByconLibs::beacon_create_queries.py Python Code Documentation

ByconLibs::beacon_generate_response (conflicted copy 2020-05-15 140411).py Python Code Documentation

ByconLibs::beacon_parse_variants.py Python Code Documentation

ByconLibs::beacon_process_handovers.py Python Code Documentation

ByconLibs::cgi_parse_variant_requests.py Python Code Documentation

ByconLibs::export_data.py Python Code Documentation

ByconLibs::pgx_modify_records.py Python Code Documentation

ByconLibs::query_execution.py Python Code Documentation

PGXJS::biosample-details.js JavaScript Code Documentation

PGXJS::publication-details.js JavaScript Code Documentation

PGXJS::publication-table.js JavaScript Code Documentation

PGXJS::subset-details.js JavaScript Code Documentation

PgyLibs::cmd_parse_args.py Python Code Documentation

PgyLibs::denormalize_records.py Python Code Documentation

PgyLibs::export_data.py Python Code Documentation

ByconLibs::cmd_parse_args.py Python Code Documentation

API::api.cgi Code Documentation

APIconfig::filter_mappings.yaml Code Documentation

APIconfig::query_params.yaml Code Documentation

BeaconPlus::ConfigLoader.pm Perl Code Documentation

BeaconPlus::DataExporter.pm Perl Code Documentation

BeaconPlus::QueryExecution.pm Perl Code Documentation

BeaconPlus::QueryParameters.pm Perl Code Documentation

BeaconPlus::SubsetQueries.pm Perl Code Documentation

BeaconPlusServer::beacondeliver.cgi Perl Code Documentation

BeaconPlusServer::beaconinfo.cgi Perl Code Documentation

BeaconPlusServer::beaconresponse.cgi Perl Code Documentation

Bycon::byconplus.py Python Code Documentation

Bycon::cytomapper.py Python Code Documentation

Bycon::pgx_cmd_modify_biosamples.py Python Code Documentation

Bycon::pgx_create_hierarchies.py Python Code Documentation

Bycon::pgx_update_from_files.py Python Code Documentation

Bycon::pgx_update_geolocs.py Python Code Documentation

Bycon::pgx_update_mappings.py Python Code Documentation

Bycon::pgxport.py Python Code Documentation

Coordinate use for Beacon Queries

Generating a publication statistics plot using the Progenetix API