Scripts and code snippets used during the development of Ninetails package.
Code below allows to pull docker image containing all necessary dependencies & resources to run the ninetails package. This docker does not contain nanopolish and guppy software.
docker pull ghcr.io/nemitheasura/ninetails-docker:latest
Note
This image does not contain Guppy, Nanopolish, minimap2, samtools and other software which is not directly linked with the Ninetails pipeline.
This command launches docker with RStudio: (username: rstudio, password:123)
docker run -it -p 8787:8787 -e PASSWORD=123 --rm r-ninetails
The access to RStudio is provided through the web browser: http://localhost:8787/ (username: rstudio, password:123).
The Training_dataset_preparation.Rmd contains steps for preparing dataset to training the model for neural network.
The finetunings_script.R controlled hyperparameters. The model was trained with Model_finetunings.Rmd
Note
For detailed documentation including explanation of additional dataprocessing and datavis features see Ninetails' Wiki
Nanopolish version containing subprogram nanopolish polya-moderna for identification of mΨCmΨAG pentamer at the 3'end of mRNA-1273 vaccine poly(A) tail. This version of Nanopolish was used in our preprint.
Please cite this repo as: Gumińska, N., Kulińska-Matylla, K., Krawczyk, P. S., Maj, M., Orzeł, W., Mackiewicz, Z., Brouze, A., Mroczek, S., & Dziembowski, A. (2024). LRB-IIMCB/ninetails_processing: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.13310035
Ninetails has been developed in the Laboratory of RNA Biology (Dziembowski Lab) at the International Institute of Molecular and Cell Biology in Warsaw.