API::api.cgi Code Documentation

APIconfig::filter_mappings.yaml Code Documentation

APIconfig::query_params.yaml Code Documentation

Articles with Genome Profiles in Progenetix

This page lists all publications for whioch the Progenetix database contains sample-specific genome profiles.

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 Changes

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

Beaconplus Data / Query Model

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

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::cmd_parse_args.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

CURIE Prefix Remapping - NCIT & PMID

Data Pages

Directories and File Structure

The Progenetix Jekyll template modifies the standard Jekyll file structure.

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.

Local Jekyll based website generation

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

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

Progenetix Oncogenomic Knowledge Resource

The Progenetix database provides an overview of copy number abnormalities in human cancer.

Progenetix Publication Collection

The current page lists articles describing whole genome screening (WGS, WES, aCGH, cCGH) experiments in cancer, registered in the Progenetix publication collection.

Progenetix segment file format

Publication Details

Publication Pages

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.

User File Uploads