/puffin_manuscript

Primary LanguageJupyter Notebook

Puffin Manuscript

This repository contains the code and data required for reproducing the analyses in the Puffin manuscript. For using Puffin and training Puffin models, please visit our main repository. For most use cases, we highly recommend running Puffin from our webserver, tss.zhoulab.io or puffin.zhoulab.io.

Most of the analyses code are provided in jupyter notebook format. Each jupyter notebook contains a series of analyses and typically generates multiple plots for related analyses.

The jupyter notebooks are grouped by topics:

Dependencies

Other than Puffin dependencies, you will also need jupyter, rpy2 python packages which can be installed with Anaconda or pip. For R packages, we will use data.table, ggplot2, patchwork, ggridges, ggrastr, ggthemes, and ggExtra.

For training Puffin-D, you need to install the custom_target_support branch of Selene

git clone https://github.com/kathyxchen/selene.git
cd selene
git checkout custom_target_support
python setup.py build_ext --inplace
python setup.py install 

Data

You will need resource files for reproducing the analyses, and we have provided these files through Zenodo and can be downloaded using the commands below

#under the puffin_mansucript directory
wget https://zenodo.org/record/7954971/files/resources.tar.xz
tar xf ./resources.tar.xz