amirmohan / sprout Goto Github PK
View Code? Open in Web Editor NEWSPROUT is a machine learning tool to predict the DNA repair outcome in CRISPR experiments.
License: Apache License 2.0
SPROUT is a machine learning tool to predict the DNA repair outcome in CRISPR experiments.
License: Apache License 2.0
dear sir,
Can SPROUT output the insertion/deletion position on the target sequence?
Just like FORECasT and inDelphi.
best
likuan
Hello,
Is it possible to get an estimation of the editing efficiency using only the gRNA?
looking at the code I thought it could be done like this:
m_frac_total_del = pickle.load(open('models/fraction_total_deletions_other_cells.p', 'rb'))
m_frac_total_ins = pickle.load(open('models/fraction_total_insertions_other_cells.p', 'rb'))
frac_total_del = 100 * float(m_frac_total_del.predict(sequence_pam_per_gene_grna)[0])
frac_total_ins = 100 * float(m_frac_total_ins.predict(sequence_pam_per_gene_grna)[0])
p_edit_eff = frac_total_ins + frac_total_del
Although i did see there's a commented out line where frac_total_del is calculated like this:
print "Fraction of total reads with deletion \t\t %.0f %%" % (frac_total_ins(100/(frac_mutant_ins) -1))*
where the bold part is frac_total_del.
Can you tell me if the way I calculate the editing efficiency (p_edit_eff ) is correct? or how to do so if it isn't?
Thanks!
How to obtain benchmark datasets to reproduce the ML results of SPROUT?
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.