DeepAdapter

A self-adaptive and versatile tool for eliminating multiple undesirable variations from transcriptome

Codes and tutorial for A self-adaptive and versatile tool for eliminating multiple undesirable variations from transcriptome.

Installation

Please install it with

$ pip install deepadapter

Get started

Before runing the codes, download our tutorials.

• DA-Example-Tutorial.ipynb: the tutorial of re-training DeepAdapter using the example dataset (click here to download);
• DA-YourOwnData-Tutorial.ipynb: the tutorial of training DeepAdapter using your own dataset (click here to download).

Re-train DeepAdapter with the provided example datsets or your own dataset

Step 1: create a new conda environment

$ # Create a new conda environment
$ conda create -n DA python=3.9
$ # Activate environment
$ conda activate DA

Step 2: install the package with pip

$ # Install the our package
$ pip install deepadapter

Step 3: launch jupyter notebook and double-click to open tutorials

$ # Launch jupyter notebook
$ jupyter notebook

After opening the tutorials, please press Shift-Enter to execute a "cell" in .ipynb.