Cptac

This release includes additional bug fixes, and provides the option of using Welch's t test instead of Student's t test in the cptac.utils.wrap_ttest function, by passing `False` to the `equal_var` parameter.

This patch release fixes a bug in the join_omics_to_mutations function that arose due to a change in the way pandas works. The bug caused an exception to be thrown when the function was executed with the mutations_filter parameter set to `None`. It is now fixed.

This patch release handles password restrictions applied to the BRCA and GBM datasets from an external source. Additionally, the following changes and enhancements were added:

- Added Dataset.multi_join fuction
- Added tissue_type parameter for metadata getters
- Added clinical column to show that all GBM tumors are stage IV (by definition)
- Renamed/combined utils functions:
- Combined:
get_protein_pathways => get_pathways_with_proteins, database="wikipathways"
search_reactome_pathways_with_proteins => get_pathways_with_proteins, database="reactome"
search_reactome_proteins_in_pathways => get_proteins_in_pathways, database="reactome"
get_proteins_in_pathway => get_proteins_in_pathways, database="wikipathways"

- Renamed:
list_pathways => list_pathways_wikipathways

Updated LSCC data, including circular_RNA and ubiquitinomics.

We also moved the `DataSet.reduce_multiindex` and `DataSet.search` functions to be part of the `cptac.utils` sub-module, instead of members of the `DataSet` class. You can now access those functions as `cptac.utils.reduce_multiindex` and `cptac.utils.search`, respectively. We also added an optional `quiet` parameter to `reduce_multiindex`.

We also renamed the abstract `DataSet` class to `Dataset`.

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.