ctwseurat

Generate and Upload Cell Type Worksheets to the UCSC Cell Atlas from a seurat object.

If you want to generate a worksheet from a scanpy object or tsv files, use ctwpy instead.

What is a Cell Type Worksheet?

A Cell Type Worksheet is an application designed to ease the burden of manual cell type annotation from single cell mRNA sequencing experiments. It lets you explore the specificity of markers across clusters and label the clusters with a cell type annotation.

The web application provides three interactive components for this goal:

1. An editable dot plot visualizing marker specificity and cell type annotation across all clusters.
2. A scatter plot visualizing gene expression across all cells.
3. A table of gene metric rankings per cluster.

Here's a rough visual of the layout of the application, the gene metrics are explored via the table at the bottom.

This python package manipulates a seurat object into the ctw format and provides an avenue for uploading a worksheet to the UCSC Cell Atlas.

Requirements

python3.4+git, pip, and virtualenv, R

Install

If you haven't done so already, head over to the Cell Atlas registry and make an account, remember to answer the confirmation email. You'll be using your email and password to upload data to the server.

Clone the repository and make a virtual environment.

git clone https://github.com/Stuartlab-UCSC/ctwseurat.git
cd ctwseurat
# Create a python3 virtual environment to install the package in.
virtualenv -p $(which python3) env

Once inside your virtual environment use pip3 to install dependencies.

# Enter virtual environment
source env/bin/activate
# Use pip to install the ctwingest dependency
pip3 install --editable git+git://github.com/Stuartlab-UCSC/ctwingest.git#egg=ctwingest
# Use pip to install this package
pip3 install --editable .

Now you'll be able to access the applications command line interface. The command line interface is available anytime you enter the environment.

Command Line Interface

# Enter virtual environment
source env/bin/activate

# Check out the help documentation:
ctw-from-seurat --help

ctw-upload --help

# Create a Cell Type Worksheet formatted file from a seurat object.
ctw-from-seurat worksheet-name s3

# Send the created Cell Type Worksheet to the UCSC Cell Atlas.
ctw-upload worksheet-name.ctw.tgz credentials.json

To upload a worksheet to the server, you'll notice the credentials.json file is necessary. Use our example for a starting place.