kuangda/sc-transmogrifier repository overview

⁠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.

⁠Features List

• SeuratRDS -> h5seurat -> h5ad
• h5ad -> h5seurat -> SeuratRDS

⁠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