Comments (4)
Questions about Kipoi output are best directed to the leaders of that project; I’m not familiar with how they’re using Basenji.
For predictions relative to a gene annotation, see this tutorial https://github.com/calico/basenji/blob/master/tutorials/genes.ipynb
from basenji.
thanks for your reply. I have tried the GitHub basenji prediction with basenji_sed.py. It successfully gave me the expression results. However, I'm not sure what's the definition of gene expression. I'm curious that in the publication it seems the training results are the 128 bin coverage for different cell types. So how does basenji link the coverage with the expression? Does this method use TSS coverage to predict the expression? I suppose here the gene expression level is not the FPKM score.
from basenji.
Yes, it’s using predicted activity in the 128 bp bin that covers the gene’s TSSs to describe its expression. I have a preprocessing step that takes in a GTF to determine those positions.
from basenji.
Thank you for the explanation.
from basenji.
Related Issues (20)
- Pre-process tutorial file not working HOT 2
- tutorial training with --sample 0.05 HOT 3
- Making Akita predictions for different bin size HOT 2
- Attention layer HOT 4
- Seeking Guidance on bam_cov.py Parameters HOT 2
- When using Akita for single-cell prediction on the HCT116 cell line, the Pearson correlation coefficient is much lower. HOT 8
- Akita: Loading weights for newer models results in mismatch HOT 2
- Issue with final matrix?
- OOM issue
- Reproduce the Enformer's input sequences split HOT 1
- Prepare data HOT 1
- Problems during model training. HOT 7
- Tensorflow / Traceback error. HOT 2
- Basenji installation issues HOT 4
- Question about the preprocessing script bam_cov.py HOT 1
- basenji_read overflow HOT 1
- Error from basenji import genome HOT 1
- Question of expected data HOT 1
- AssertionError, Basenji_test.py 'Conv1D' object has no attribute 'input_shape' HOT 1
- akita train error
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from basenji.