Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of geniebpc

geniebpc - genieBPC 2.0.1

  • 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.

- R
Published by jalavery over 1 year ago

geniebpc - genieBPC 1.1.1

  • 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()

Data Release Updates

  • 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.

- R
Published by jalavery almost 2 years ago

geniebpc - v1.1.0.9004

  • 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)

  • Update tests to test across all data releases (#56)

  • Fix bug related to radiation therapy data not being returned in create_analytic_cohort()

- R
Published by jalavery over 2 years ago

geniebpc - v1.1.0

  • 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

- R
Published by jalavery about 3 years ago

geniebpc - v1.0.1

This is the version of the release that corresponds to v1.0.1 on CRAN.

Updates to documentation, messaging, and function internals.

- R
Published by jalavery over 3 years ago

geniebpc - v1.0.0

This is the version of the release that corresponds to v1.0.0 on CRAN.

- R
Published by jalavery over 3 years ago

geniebpc - v0.1.0

Initial release of the {genieBPC} package. This version of the package has a dependency on the {synapser} package.

- R
Published by jalavery over 3 years ago