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kuang-da / sc-transmogrifier

A containerized tool for converting single-cell data between Seurat objects (R) and AnnData (Python) formats.
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sc-transmogrifier

A containerized tool for converting single-cell data between Seurat objects (R) and AnnData (Python) formats.

Overview

sc-transmogrifier is a utility designed to facilitate the transformation of single-cell data between the popular R-based Seurat objects and Python-based AnnData objects. This enables researchers to easily switch between different single-cell analysis workflows and tools within the R and Python ecosystems. The conversion code is primarily based on SeuratDisk. The main contribution of this project is to provide a standalone and self-contained service, including necessary patches (e.g., issue #1) for format conversion. This is particularly convenient when working with large datasets or when you want to isolate conversion-related packages from your project environment.

image

Features List

Installation

Docker

To pull the docker image, use the following command:

docker pull kuangda/sc-transmogrifier

Test the functionality of the image with this command:

docker run --rm kuangda/sc-transmogrifier bash test.sh

Sigularity

To be added.

Usage

To run the docker container, use the following command, replacing <LOCAL INPUT DIR>, <LOCAL OUTPUT DIR>, and <LOCAL GIT REPO>: with the appropriate paths:

docker run --rm\
 -v <LOCAL INPUT DIR>:/app/data\
 -v <LOCAL OUTPUT DIR>:/app/out\
 -v <LOCAL GIT REPO>:/app/sc-transmogrifier\
 kuangda/sc-transmogrifier\
 bash /app/sc-transmogrifier/run-seurat2ann.sh <RDS FILE> <ASSAY NAME> <RAW ONLY>

Example

The following command demonstrates how to run the container with specific input and output directories:

docker run --rm\
 -v /mnt/nvme-1/2-hubmap/spatial/ref-scrna/data/ft:/app/data\
 -v /mnt/nvme-1/2-hubmap/spatial/ref-scrna/out/ft:/app/out\
 -v /mnt/nvme-1/2-hubmap/sc-transmogrifier:/app/sc-transmogrifier\
 kuangda/sc-transmogrifier\
 bash /app/sc-transmogrifier/run-seurat2ann.sh /app/data/FT_wnn_integrated-0713.RDS RNA TRUE

Docker Environment

VSCode Devcontainer

The development environment is managed by .devcontainer configuration.

Update Docker Image

To rebuild and push the docker image to DockerHub, use the following command:

bash .docker/docker-build.sh