Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/babinyurii/sgrna-mismatch-activity

predicting sgRNA mismatch activity using keras

https://github.com/babinyurii/sgrna-mismatch-activity

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: springer.com, nature.com
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.3%) to scientific vocabulary

Keywords

crispr keras keras-tensorflow sgrna
Last synced: 6 months ago · JSON representation

Repository

predicting sgRNA mismatch activity using keras

Basic Info
  • Host: GitHub
  • Owner: babinyurii
  • Language: Jupyter Notebook
  • Default Branch: master
  • Homepage:
  • Size: 41 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Topics
crispr keras keras-tensorflow sgrna
Created about 6 years ago · Last pushed almost 3 years ago

https://github.com/babinyurii/sgRNA-mismatch-activity/blob/master/ 

# Predicting sgRNA mismatch activity using Keras

- based on the method described in the article: [Jost, M., Santos, D.A., Saunders, R.A. et al. Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs. Nat Biotechnol 38, 355364 (2020). https://doi.org/10.1038/s41587-019-0387-5](https://www.nature.com/articles/s41587-019-0387-5)

- **[the workflow described by the authors of the article](https://static-content.springer.com/esm/art%3A10.1038%2Fs41587-019-0387-5/MediaObjects/41587_2019_387_MOESM4_ESM.html)**

- the 'Table_S8_machine_learning_input.txt' which contains training dataset can be found [in this repo's table folder](https://github.com/babinyurii/sgRNA-mismatch-activity/tree/master/tables)

### Comparison of measured and predicted activities measured by neural network. r^2 = 0.62 (in the article r^2 = 0.65)
![correlation](https://github.com/babinyurii/sgRNA-mismatch-activity/blob/cd759ca0910473b5dd1c982be0d713535efff9d6/plots/correlation.PNG)

### some plots showing sgRNA activity prediction. The activity is changed due to mismatch type and  position

![aid](https://raw.githubusercontent.com/babinyurii/sgRNA-mismatch-activity/master/plots/aid.png)

![apobec3a](https://raw.githubusercontent.com/babinyurii/sgRNA-mismatch-activity/master/plots/apobec3a.png)

![apobec3b](https://raw.githubusercontent.com/babinyurii/sgRNA-mismatch-activity/master/plots/apobec3b.png)

![apobec3g](https://raw.githubusercontent.com/babinyurii/sgRNA-mismatch-activity/master/plots/apobec3g.png)

Owner

  • Name: Yuriy Babin
  • Login: babinyurii
  • Kind: user

GitHub Events

Total
Last Year