genieBPC 2.2.0

genieBPC 2.1.1

Add CRC v3.1-consortium, RENAL v1.1-consortium, and BrCa v1.0-public data releases (#148)
Update tests to use setup.R file and to only run current data releases on CRAN and GitHub Actions (all data releases are tested when running locally)

Update create_analytic_cohort() to allow cohorts to be created based on multiple cancer types. Previously, only one cancer type at a time was permitted.
Update GitHub actions to v4
Breaking change: Remove access to GENIE BPC data on Synapse via username and password per updated Synapse requirements. Access to the data is now via Personal Access Token (PAT) only.
Deprecate functions allowing data access by username and password.
- Remove .get_token_by_username() function
- Remove .get_token_by_pat() function (it is now redundant with .get_synapse_token())
- added .verify_pat_works() helper function

Update ‘cohort’ parameter of pull_data_synapse() and synapse_version() to not be case-sensitive (#120)
synapse_version(most_recent = TRUE) now returns one row per cohort, as opposed to one row per cohort and type of data release (consortium vs public) (#128)
Update drug_regimen_list lookup table to include drug names by data release, as opposed to by cohort. It is possible that drug names were modified slightly across data releases (#132)
NEW FEATURE: Users can now pass their Personal Access Token (as well as username/ password) to set up authentication for accessing all data. (#119)
BREAKING CHANGE: Users must use set_synapse_credentials() at the top of all scripts and explicitly set username/password or PAT for each session.
Added NSCLC v3.1-consortium release (#137)
Read in structural variant files for NSCLC v2.2-consortium, CRC v1.3-consortium, and Bladder v1.2-consortium. For more information on structural variant data, see: https://docs.cbioportal.org/file-formats/#structural-variant-data.

Updated code for default institution in create_analytic_cohort() to fix bug if the cohort = “Prostate” (#130)
Add ‘cohort’ parameter to synapse_version() to enable the user to subset by cohort(s) of interest
Updated genieBPC::nsclc_test_data to ensure unique sample ids for CNA file.
Updated genieBPC::nsclc_test_data to randomly sample from cancer diagnosis dataset, stratified by stage, and incorporate genomic data into dataset.
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)
Update tests to test across all data releases (#56)
Fix bug related to radiation therapy data not being returned in create_analytic_cohort()

Added BLADDER v1.2-consortium release
Added NSCLC 2.3-consortium release
Added CRC v1.3-consortium release
Removed NSCLC 2.1-consortium release - Due to the inadvertent inclusion of data indicative of ages over 89 for data associated with the Project GENIE BioPharma Collaborative, this release was replaced with the NSCLC 2.3-consortium release.
Removed CRC v1.1-consortium release - Due to the inadvertent inclusion of data indicative of ages over 89 for data associated with the Project GENIE BioPharma Collaborative, this release was replaced with the newly added CRC v1.3-consortium release.
Removed CRC v1.2-consortium release - Due to the inadvertent inclusion of data indicative of ages over 89 for data associated with the Project GENIE BioPharma Collaborative, this release was replaced with the newly added CRC v1.3-consortium release.

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

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).

Changed print() to message() in select_unique_ngs()
Removed TramineR from dependencies file (issue #50)
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