Added analysis folder and protein_analysis.py#176

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AriaAgarwal wants to merge 34 commits intogyorilab:mainfrom AriaAgarwal:Protein-Analysis

+211,471-446

Commits on Oct 1, 2024

Adding route handlers for each type of analysis which use the imported analysis functions

Prasham Marfatia
authored and
kkaris
committed
Implement discrete_gene_analysis() and refactor code

AriaAgarwal
authored and
kkaris
committed
Take curation into account in statement assembly

bgyori
authored and
kkaris
committed
Add statement evidence and update notebook

bgyori
authored and
kkaris
committed
Clean up notebook and add outputs

bgyori
authored and
kkaris
committed
added bar chart visualizations

AriaAgarwal
authored and
kkaris
committed
deleted unnecessary comments

AriaAgarwal
authored and
kkaris
committed
deleted notebook block from .py file

AriaAgarwal
authored and
kkaris
committed
Refactor functions to accept source protein as a list

AriaAgarwal
authored and
kkaris
committed
return a dictionary of results from run_explain_downstream_analysis()

AriaAgarwal
authored and
kkaris
committed
Create jinja template for results

AriaAgarwal
authored and
kkaris
committed
cleaned up code

AriaAgarwal
authored and
kkaris
committed
refactored code to create tabs

AriaAgarwal
authored and
kkaris
committed
Refactored code to accept source_protein as a string

AriaAgarwal
authored and
kkaris
committed
Added two tabs for shared pathways and go terms

AriaAgarwal
authored and
kkaris
committed
Add margins and regorganize tab order

AriaAgarwal
authored and
kkaris
committed
Arrange Plots and Delete Tabs

AriaAgarwal
authored and
kkaris
committed
Refactor shared pathways function

AriaAgarwal
authored and
kkaris
committed
This is the results.html file

AriaAgarwal
authored and
kkaris
committed
Reset table indexes

AriaAgarwal
authored and
kkaris
committed
Make tables interactive

AriaAgarwal
authored and
kkaris
committed
Using full protein list for analysis

AriaAgarwal
authored and
kkaris
committed
Updated results with full protein list, no change to notebook

AriaAgarwal
authored and
kkaris
committed
Read html file content and uncomment curation lines

AriaAgarwal
authored and
kkaris
committed
Clean INDRA statement presentation

AriaAgarwal
authored and
kkaris
committed
Rebase cleanup: Set to None if no shared proteins
kkaris
committed
Rebase cleanup: Just pass hgnc id list directly to discrete analysis
kkaris
committed
Rebase cleanup: various docstring fixes
kkaris
committed
Rebase cleanup: rename dict keys
kkaris
committed
Rebase cleanup: set indra path analysis to True
kkaris
committed
Specify in docstring that iterable is OK
kkaris
committed
Update notbook with writing results.html and re-run
kkaris
committed
Update results.html from notebook re-run
kkaris
committed

Commits on Oct 3, 2024

Add blurbs to INDRA html tabs
AriaAgarwal
committed

Provide feedback

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Added analysis folder and protein_analysis.py#176

Commits on Oct 1, 2024

Adding route handlers for each type of analysis which use the imported analysis functions

Implement discrete_gene_analysis() and refactor code

Take curation into account in statement assembly

Add statement evidence and update notebook

Clean up notebook and add outputs

added bar chart visualizations

deleted unnecessary comments

deleted notebook block from .py file

Refactor functions to accept source protein as a list

return a dictionary of results from run_explain_downstream_analysis()

Create jinja template for results

cleaned up code

refactored code to create tabs

Refactored code to accept source_protein as a string

Added two tabs for shared pathways and go terms

Add margins and regorganize tab order

Arrange Plots and Delete Tabs

Refactor shared pathways function

This is the results.html file

Reset table indexes

Make tables interactive

Using full protein list for analysis

Updated results with full protein list, no change to notebook

Read html file content and uncomment curation lines

Clean INDRA statement presentation

Rebase cleanup: Set to None if no shared proteins

Rebase cleanup: Just pass hgnc id list directly to discrete analysis

Rebase cleanup: various docstring fixes

Rebase cleanup: rename dict keys

Rebase cleanup: set indra path analysis to True

Specify in docstring that iterable is OK

Update notbook with writing results.html and re-run

Update results.html from notebook re-run

Commits on Oct 3, 2024

Add blurbs to INDRA html tabs