UcecConf - Added version 2.0, which has the following changes: 1. Recalculated WGS-based CNV using the same pipeline 2. Updated CNV-H identification by the new CNV (1 POLE is CNV-H) 3. Updated the ABSOLUTE tumor purity by the new CNV 4. Fixed a bug for RNAseq data processing 5. Updated ESTIMATE score derived from RNAseq data 6. Added category level somatic mutation NOTE: UcecConf 2.0 has the following minor issues that need correction and will be updated: C3L-05848 with tumor size -2. C3L-02747 and C3N-00155 with tumor size 0. C3L-03143 with a height 2 cm and derived a BMI 287456.75
BRCA: Column "Tumor.Stage" renamed to "Stage" in brca clinical data
Pancan: -Function list_sources_data() renamed to list_data_sources() -Adjust argument order for get_deconvolution() to be consistent with other functions -Add readme files to help in choosing desired pipeline
Other: -Bugfix for cptac.utils function get_protein_interactions_bioplex -Use case 7 notebook updated
0.9.6
Updates to Pancan Most use cases have been updated to work with the latest version of this package and any packages used with them The endometrial confirmatory data has been updated to 1.2
0.9.5
This release adds a ubiquitinomics getter function for access to that data, along with restoring the somatic mutation data to the brca dataset, which was unintentionally left out. The tutorials have also been updated to reflect the latest version of the package.
0.9.4
Patch release for bug fixes:
-Ucecconf is working again -Brca should load correctly now -The mygene dependency was added
0.9.3
Patch release for bugfixes
0.9.2
Updated the package to use the most recent data for three types of cancer