Tutorials of Scribe Python package usage cases
aristoteleo / scribe-python-notebooks Goto Github PK
View Code? Open in Web Editor NEWTutorials of Scribe Python package usage cases
Tutorials of Scribe Python package usage cases
Thank you!
Currently the notebook includes an application on the simulation system from scanpy. The simulation system used in the Scribe paper should also included, ideally full types of data should be included (real time, RNA velocity, pseudotime and live-image).
Hi Xiaojie,
A really cool tool for building the network, thanks for putting it together.
When running NASC_seq_Jurkat_T_cell_demo.ipynb with the demo data I was not able to calculate causality score running Scribe(adata, t0_key='spliced', t1_key='unspliced').
IndexError Traceback (most recent call last)
in
----> 1 Scribe(adata, t0_key='spliced', t1_key='unspliced')
/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/Scribe/Scribe.py in causal_net_dynamics_coupling(adata, TFs, Targets, guide_keys, t0_key, t1_key, normalize, drop_zero_cells, copy)
127 z_orig = [[i] for i in z_orig]
128
--> 129 causal_net.loc[g_a, g_b] = cmi(x_orig, y_orig, z_orig)
130
131 adata.uns['causal_net'] = {"RDI": causal_net.fillna(0)}
/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/Scribe/information_estimators.py in cmi(x_orig, y_orig, z_orig, normalization, k)
144 N = len(x)
145
--> 146 dx = len(x[0])
147 dy = len(y[0])
148 dz = len(z[0])
IndexError: list index out of range
Fixed with your advise by setting
drop_zero_cells=False in the function causal_net_dynamics_coupling
Scribe(adata, t0_key='spliced', t1_key='unspliced', drop_zero_cells=False)
Hope this report maybe useful for others
Thanks!
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.