Cptac

Join functions now include a "tissue_type" parameter to allow specification for "tumor","normal", or defaults to "both" types of cell tissue data to be returned.

Several utils have been added with this release, including:
"wrap_pearson_corr", which returns a dataframe with columns comparison, correlation coefficient, and p value from a given dataframe.

"get_interacting_proteins_wikipathways", which takes a given protein and finds a list of all proteins that interact with it according to wikipathways.

"get_protein_pathways", which takes a given protein and uses wikipathways to find the pathways that the protein is involved in.

"list_pathways", which returns all possible pathways from wikipathways.

"get_proteins_in_pathway", which takes a pathway and lists all proteins involved in it.

Bug fixes for missing dataframe in lscc version 1.0 data.

We added a "quiet" parameter as part of our join functions in order to allow users to quiet the warnings produced when filling dataframes with NaNs.

We also added a "how" parameter to allow users to specify their desired join type, whether inner, outer, left or right.

Also included is a functionality to specify which sample type users want to be returned in a dataframe, whether tumor, normal, or both.

This release fixes a bug that dropped all of the LUAD followup data. It also changes the data loaders so that when the followup table includes samples that aren't anywhere else in the dataset (because they're from a different cohort), those samples are kept and not dropped like they were previously.

This release also switches the install to require pandas 1.0.0 or greater.

This release adds the LSCC dataset (password protected). It also includes the DataSet.get_genotype_all_vars function, as well as minor formatting improvements.

This release stops using generated Sample IDs (e.g. S001, S002, etc.) for indexing tables, and instead uses the original CPTAC Patient IDs (e.g. C3L-00078, etc.). Normal samples are indicated by a ".N" appended to the end of the Patient ID (e.g. "C3L-00078.N") in all datasets.

This release also includes updates to the GBM, LUAD, and HNSCC datasets. We also have added a new "followup" table in all datasets besides GBM, which contains followup data for the patients in the cohort.

Finally, this release includes increased access to datasets. The BRCA dataset now has no access restrictions. The GBM and LUAD datasets are both under publication embargo, but no longer require passwords for access.

This release contains the newest GBM data freeze (2.1), and adds the sample immune classification to the CCRCC clinical table. We also fixed a small bug in utils.get_frequently_mutated that was preventing it from working properly with the HNSCC dataset.