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 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 tosunburstR::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()
tomessage()
inselect_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 infetch_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