CountCorrect

A method for background removal from Nanostring WTA data

Notebooks

See Background Removal with CountCorrect

Installation

You will first need to configure an appropriate conda environment and then you can install countcorrect directly from github. How to do this is explained below.

1. Configure countcorrect conda environment

If you do not have conda please install Miniconda first:

cd /path/to/software
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
# use prefix /path/to/software/miniconda3

Now there are two ways you can configure the 'countcorrect' conda environment:

1. Method 1 (preferred): Create environment from file

Create countcorrect environment from file, which will install all the required conda and pip packages:

git clone https://github.com/BayraktarLab/CountCorrect/
cd CountCorrect
conda env create -f environment.yml

1. Method 2: Create conda environment manually

Create conda environment manually using first conda:

conda create -n countcorrect python=3.7 numpy pandas jupyter scanpy \
ipython seaborn matplotlib \
pygpu --channel bioconda --channel conda-forge

And then install these packages with pip:

pip install "pymc3>=3.8,<3.10" torch arviz==0.11.1 adjustText

2. Install countcorrect package

Finally you can install countcorrect:

 pip install git+https://github.com/BayraktarLab/CountCorrect/