Changelog • genieBPC

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)

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

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).

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