Associate expression data with Transcript/Junction/Exon objects

sheynkman-lab / biosurfer

"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.

MIT License

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Associate expression data with Transcript/Junction/Exon objects #72

Open jsaquing opened 3 years ago

jsaquing commented 3 years ago

Types of queries that need to be supported:

condition + objects --> expression for each object under condition
object + conditions --> expression for object under each condition

Possible low-level implementations:

for a given condition, map each object to its expression data
for a given object, map each condition to corresponding expression data

jsaquing commented 3 years ago

So far I've found keeping expression data in a pandas dataframe (indexed by accession) has been very flexible... perhaps the integration with Biosurfer will consist more of helper functions that encapsulate common operations on the dataframe (e.g. getting the expressions for a list of Transcript objects)? Or maybe the Expression class can just be a specialized container for a dataframe?