Skip to contents

genieBPC (development version)

  • Updated genieBPC::nsclc_test_data to ensure unique sample ids for CNA file.

  • Updated README and ‘Pull Data Synapse Vignette’ to clarify instructions for registering for a ‘Synapse’ account (#100, #105)

  • Add publications (#96, #110)

  • Add information about genomic differences between genomic data downloaded from cBioPortal versus Synapse (#92)

genieBPC 1.1.0

CRAN release: 2023-03-03

  • Add PANC v1.1-consortium, Prostate v1.1-consortium, BrCa 1.2-consortium, PANC v1.2-consortium, Prostate v1.2-consortium, CRC 2.0-public data releases

  • Removed fetch_samples() function (#91)

  • Updated pull_data_synapse() to read “NA” as NA values instead of as character “NA” so that CNA columns are numeric, as expected (#88)

  • Ensure consistent order of datasets returned from calls to pull_data_synapse()

  • Added citations & links to GENIE BPC publications to README

genieBPC 1.0.1

CRAN release: 2022-10-27

  • Updates to select_unique_ngs() documentation and vignettes, as well as clarification of the messaging returned when the function is run (#57)

  • Update selecting functions to account for tidyselect v1.2.0 release (issue #83)

  • Documentation updates following Bioinformatics reviewer comments (issue #75)

  • Update drug_regimen_sunburst() to pass additional arguments to sunburstR::sunburst() (issue #71)

  • Added CRAN installation instructions to README (issue #72)

  • Add CRAN badge to README (issue #69)

  • Update handling of missing data when reading in csv files in pull_data_synapse() so that missing data is stored as NA and not as “” (issue #73).

genieBPC 1.0.0

CRAN release: 2022-08-14

  • Changed print() to message() in select_unique_ngs()

  • Removed TramineR from dependencies file (issue #50)

  • Incorporated the most recent public and consortium data releases (issue #42)

  • Removed synapser from dependencies file (issue #45)

  • Fixed cpt_sample_type/sample_type issue in fetch_samples.R (issue #43)

  • Added .is_connected_to_genie() to replace .check_synapse_login() and return logical TRUE/FALSE. This is an internal function that can be used to trigger tests/checks as needed and will hopefully allow the package to now pass the CRAN checks.

  • Added drug names for breast cancer cohort

  • Update examples to use test data, when possible

genieBPC 0.1.0

  • Added a file to track changes to the package.