Published June 20, 2023 | Version v0.6.1-beta
Software Open

PediatricOpenTargets/OpenPedCan-api: v0.6.1-beta

Authors/Creators

  • 1. Children's Hospital of Philadelphia

Description

Changelog for this release version v0.6.1-beta Changed
  • Updated database using OpenPedCan-analysis v12 final release data.
  • Changed db/build_db.sh to download OpenPedCan-analysis api-data using db/build_tools/download_api_data.sh.
  • Changed db/build_tools/build_db_docker_cmd.sh to compress intermediate CSV files.
Added
  • Added db/build_tools/download_api_data.sh to download OpenPedCan-analysis api-data.
v0.6.0-beta Changed
  • Changed the interface of get_gene_tpm_tbl function:
    • Added a required parameter tcga_sample_group.
  • Changed the interface of get_tpm_endpoint_tbl function:
    • Added a required parameter tcga_sample_group.
  • Updated db/db.Dockerfile PostgreSQL docker image to version 12.13.
Added
  • Added OpenPedCan-analysis TCGA TPM data to the database.
  • Added the following TCGA expanded TPM boxplot and summary table endpoints:
    • /tpm/gene-disease-tcga/plot
    • /tpm/gene-disease-tcga/json
    • /tpm/gene-disease-tcga-gtex/plot
    • /tpm/gene-disease-tcga-gtex/json
    • /tpm/gene-all-cancer-tcga/plot
    • /tpm/gene-all-cancer-tcga/json
    • /tpm/gene-all-cancer-tcga-gtex/plot
    • /tpm/gene-all-cancer-tcga-gtex/json
  • Added tests in tests/r_test_scripts/test_endpoint_http.R to test the added TCGA expanded TPM boxplot and summary table endpoints.
v0.5.3-beta Changed
  • Updated database using OpenPedCan-analysis v11 TPM data and independent sample lists.
  • Updated tests/r_test_scripts/test_endpoint_http.R according to OpenPedCan-analysis v11 TPM data.
v0.5.2-beta Changed
  • Updated database using v10 differential gene expression (DGE) data.
  • Installed libxml2 in Dockerfile.
  • Updated tests for DGE heatmap endpoints, according to v10 DGE data.
v0.5.1-beta Changed
  • Changed the interfaces of the following endpoints by adding two required parameters, includeBoxplot and boxplotYAxisScale, to determine whether to add boxplots with certain Y-axis scales on the sides of the differential gene expression (DGE) heatmaps or not.
    • /dge/top-gene-disease-gtex-diff-exp/plot
    • /dge/gene-all-cancer-gtex-diff-exp/plot
v0.5.0-beta Added
  • Added the following differential gene expression (DGE) endpoints to transfer DGE heatmap PNG plots and JSON tables via HTTP GET method.
    • /dge/top-gene-disease-gtex-diff-exp/json: Transfer a JSON table of one disease and top differentially expressed genes.
    • /dge/top-gene-disease-gtex-diff-exp/plot: Transfer a PNG heatmap of one disease and top differentially expressed genes.
    • /dge/gene-all-cancer-gtex-diff-exp/json: Transfer a DGE JSON table of one gene and all diseases.
    • /dge/gene-all-cancer-gtex-diff-exp/plot: Transfer a DGE PNG heatmap of one gene and all diseases.
  • Added DGE database table BULK_EXP_SCHEMA.BULK_EXP_DIFF_EXP_TBL, which is declared in ../OpenPedCan-api-secrets/common_db.env and db/r_interfaces/db_env_vars.R and constructed in db/build_tools/build_db.R and db/build_tools/build_db_docker_cmd.sh.
  • Added the following R scripts to implement the added DGE endpoints.
    • src/get_one_efo_top_ensg_diff_exp_heatmap.R
    • src/get_one_efo_top_ensg_diff_exp_heatmap_tbl.R
    • src/get_one_efo_top_ensg_diff_exp_tbl.R
    • src/get_one_ensg_all_efo_diff_exp_heatmap.R
    • src/get_one_ensg_all_efo_diff_exp_heatmap_tbl.R
    • src/get_one_ensg_all_efo_diff_exp_tbl.R
  • Added tests in tests/r_test_scripts/test_endpoint_http.R to test the added DGE endpoints.

Files

PediatricOpenTargets/OpenPedCan-api-v0.6.1-beta.zip

Files (822.6 MB)

Additional details

Related works

Is supplement to
https://github.com/PediatricOpenTargets/OpenPedCan-api/tree/v0.6.1-beta (URL)