scaden 0.9.6

Cell type deconvolution using single cell data

Single-cell assisted deconvolutional network

Scaden is a deep-learning based algorithm for cell type deconvolution of bulk RNA-seq samples. It was developed at the DZNE Tübingen and the ZMNH in Hamburg. The method is published in Science Advances: Deep-learning based cell composition analysis from tissue expression profiles

A complete documentation is available here

Scaden overview. a) Generation of artificial bulk samples with known cell type composition from scRNA-seq data. b) Training of Scaden model ensemble on simulated training data. c) Scaden ensemble architecture. d) A trained Scaden model can be used to deconvolve complex bulk mixtures.

1. System requirements

Scaden was developed and tested on Linux (Ubuntu 16.04 and 18.04). It was not tested on Windows or Mac, but should also be usable on these systems when installing with Pip or Bioconda. Scaden does not require any special hardware (e.g. GPU), however we recommend to have at least 16 GB of memory.

Scaden requires Python 3. All package dependencies should be handled automatically when installing with pip or conda.

2. Installation guide

Stable version

The recommended way to install Scaden is using conda and the Bioconda channel.

You can create a conda environment for your scaden installation to minimize package conflicts:

conda create -n scaden_env --override-channels -c defaults -c conda-forge -c bioconda scaden

scaden depends on tensorflow. On conda tensorflow uses the CPU to train the networks. If you have a cuda capable GPU, you may want to install the tensorflow-gpu conda package as well so scaden uses the gpu instead:

conda activate scaden_env
conda install tensorflow-gpu

Installation with conda takes only a few minutes (2-5), depending on the internet connection.

Alternatively Scaden can be installed with pip:

# Create a virtual environment:
python3 -m venv ./venv
# Activate the virtual environment with:
source ./venv/bin/activate
# Upgrade pip and wheel:
python3 -m pip install -U pip wheel
# Install scaden:
python3 -m pip install -U scaden

We also provide a docker image with Scaden installed: https://hub.docker.com/r/kevinmenden/scaden

Webtool (beta)

Additionally, we now proivde a web tool:

https://scaden.ims.bio

It contains pre-generated training datasets for several tissues, and all you need to do is to upload your expression data. Please note that this is still in preview.

3. Demo

We provide several curated training datasets for Scaden. For this demo, we will use the human PBMC training dataset, which consists of 4 different scRNA-seq datasets and 32,000 samples in total. You can download it here: https://figshare.com/s/e59a03885ec4c4d8153f.

For this demo, you will also need to download some test samples to perform deconvolution on, along with their associated labels. You can download the data we used for the Scaden paper here: https://figshare.com/articles/Publication_Figures/8234030

We'll perform deconvolution on simulated samples from the data6k dataset. You can find the samples and labels in 'paper_data/figures/figure2/data/data6k_500_*' once you have downloaded this data from the link mentioned above.

The first step is to perform preprocessing on the training data. This is done with the following command:

scaden process pbmc_data.h5ad paper_data/figures/figure2/data/data6k_500_samples.txt

This will generate a file called 'processed.h5ad', which we will use for training. The training data we have downloaded also contains samples from the data6k scRNA-seq dataset, so we have to exclude them from training to get a meaningfull test of Scaden's performance. The following command will train a Scaden ensemble for 5000 steps per model (recommended), and store it in 'scaden_model'. Data from the data6k dataset will be excluded from training. Depending on your machine, this can take about 10-20 minutes.

scaden train processed.h5ad --steps 5000 --model_dir scaden_model --train_datasets 'data8k donorA donorC'

Finally, we can perform deconvolution on the 500 simulates samples from the data6k dataset:

scaden predict paper_data/figures/figure2/data/data6k_500_samples.txt --model_dir scaden_model

This will create a file named 'cdn_predictions.txt' (will be renamed in future version to 'scaden_predictions.txt'), which contains the deconvolution results. You can now compare these predictions with the true values contained in 'paper_data/figures/figure2/data/data6k_500_labels.txt'. This should give you the same results as we obtained in the Scaden paper (see Figure 2).

4. Instructions for use

For a general description on how to use Scaden, please check out our usage documentation.