paraCell: A novel software tool for the interactive analysis and visualization of standard and dual host-parasite scRNA-seq data

Advances in sequencing technology have led to a dramatic increase in the number of single-cell transcriptomic datasets available. In the field of parasitology these datasets typically describe the gene expression patterns of a given parasite species under specific experimental conditions, in specific hosts or tissues, or at different life-cycle stages. However, while this wealth of available data represents a significant resource for further research, the analysis of these datasets often requires significant computational skills, preventing a considerable proportion of the parasitology community from meaningfully incorporating existing single-cell data into their work. Here we present paraCell, a novel software tool that automates the advanced analysis of published single-cell data without requiring any programming ability. paraCell builds on the core functionality of cellxgene and cellxgene VIP to offer additional analysis features of value to parasitologists (see Figure 1). The software is freely available for the community for local use, and various published datasets offer examples of what paraCell can achieve.

Figure 1 | Overview of the four main options in paraCell. Advanced Gene Search - a custom gene-set is used to create a cellxgene VIP multi-gene violin plot (Plasmodium berghei dataset). Host-Parasite Interactions - selection made on the Parasite UMAP is used to update the Host UMAP (Cow-Theileria dataset). Database Integration - paraCell results table is shown alongside links to relevant external database systems (P. berghei dataset). Trajectory Inference - Slingshot trajectories drawn over PHATE space of single-cell data, enables tradeSeq to plot expression of genes over their “pseudo time” for different conditions - example relates the expression of the gene PAD2 to the progression of both trajectories in the WT and KO condition (Trypanosoma brucei dataset).

Demo datasets:

• Plasmodium berghei - https://cellatlas-cxg.mvls.gla.ac.uk/view/Pb.Combined.h5ad/
• Trypanosoma brucei - https://cellatlas-cxg.mvls.gla.ac.uk/view/Tbrucei.h5ad/

Online tutorial:

• paraCell features - https://github.com/sii-cell-atlas/paraCell/wiki
• Core VIP functionality - https://interactivereport.github.io/cellxgene_VIP/tutorial/docs

Installation instruction

1. Install miniconda if not available on server (https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html)

bash ~/Downloads/Miniconda3-latest-Linux-x86_64.sh
conda install mamba -n base -c conda-forge

2. Create and enable conda environment

git clone https://github.com/sii-cell-atlas/paraCell.git
cd paraCell

source <path to Miniconda3>/etc/profile.d/conda.sh 
conda config --set channel_priority flexible
mamba env create -n <env name, such as: paraCell> -f paraCell_conda_R.yml (local R under conda, no root privilege needed)

For Mac User, conda env create -n <env name, such as: paraCell> -f paraCell.macOS.yml

mamba env update -f r_dependencies.yml --name paraCell

conda activate <env name, such as: paraCell>
or
source activate <env name>

3. Install cellxgene by running config.sh in "paraCell" directory

./config.sh
For Mac User, ./config.macOS.sh

4. Run cellxgene by specifiying a h5ad file storing scRNA-seq data along with a host and a port, use "ps" to find used ports to spare, see https://chanzuckerberg.github.io/cellxgene/posts/launch for details.

ps -ef | grep cellxgene
Rscript -e 'reticulate::py_config()'
# Run the following command if the output of the above command doesn't point to the Python in your env.
export RETICULATE_PYTHON=`which python`
cellxgene launch --host <xxx> --port <xxx> --disable-annotations --verbose <h5ad file>

5. From web browser (Chrome is preferred, Version 87.0.4280.88 or 87.0.4280.141 is used), access http(s)://host:port

You should be able to see this in Console of Chrome Developer Tools if everything is right.

note: while spinning up the cellxgene from HPC, do NOT use qlogin. ssh directly to the server.

Updating

./update.VIPInterface.sh all # if "interface.html" or "VIPInterface.py" is modified or new code needs to go to right location, often.

./update.index_template.sh # if jsPanel is modified, very rare.