class openomics.database.annotation.ProteinAtlas(path='', file_resources=None, col_rename={'Ensembl': 'gene_id', 'Gene': 'protein_name'}, blocksize=0, verbose=False)[source][source]#

Bases: openomics.database.base.Database

Loads the database from .

Default path: . Default file_resources: {

“”: “”, “”: “”, “”: “”,


Attributes Summary

Methods Summary

get_expressions([index, type])

Returns (NX) expressions from the proteinatlas.tsv table.

load_dataframe(file_resources[, blocksize])

param file_resources

Attributes Documentation

COLUMNS_RENAME_DICT = {'Ensembl': 'gene_id', 'Gene': 'protein_name'}[source]#

Methods Documentation

get_expressions(index='gene_name', type='Tissue RNA')[source][source]#

Returns (NX) expressions from the proteinatlas.tsv table. :param index: a column name to index by. If column contain multiple values, then aggregate by median values. :param type: one of {“Tissue RNA”, “Cell RNA”, “Blood RNA”, “Brain RNA”, “RNA - “}. If “RNA - “, then select all types of expressions.

  • index

  • type


Return type

expressions (pd.DataFrame)

load_dataframe(file_resources, blocksize=None)[source][source]#
  • file_resources

  • blocksize