getwilds/dropletutils repository overview

⁠DropletUtils

This directory contains Docker images for DropletUtils, a Bioconductor package for handling and preprocessing single-cell RNA-seq data generated by droplet-based technologies such as 10x Genomics.

⁠Available Versions

• latest ( Dockerfile⁠ | Vulnerability Report⁠ )
• 1.32.0 ( Dockerfile⁠ | Vulnerability Report⁠ )

⁠Image Details

These Docker images are built from the Bioconductor 3.23 base image and include:

• DropletUtils v1.32.0: Loads raw droplet-based count data, distinguishes real cells from empty droplets (via the emptyDrops algorithm), removes barcode-swapped pseudo-cells, and downsamples reads

The images are designed to be minimal and focused on DropletUtils itself for droplet-based single-cell RNA-seq preprocessing workflows.

⁠Platform Availability

Note: This image is only built for linux/amd64 architecture. ARM64 builds are not currently available; support may be revisited in a future update.

⁠Citation

If you use DropletUtils in your research, please cite the original authors:

Lun ATL, Riesenfeld S, Andrews T, Dao TP, Gomes T, participants in the 1st
Human Cell Atlas Jamboree, Marioni JC. (2019). EmptyDrops: distinguishing
cells from empty droplets in droplet-based single-cell RNA sequencing data.
Genome Biology, 20, 63.
https://doi.org/10.1186/s13059-019-1662-y

Tool homepage: https://bioconductor.org/packages/DropletUtils⁠

Source repository: https://github.com/MarioniLab/DropletUtils⁠

Note: This Docker image is simply a containerized version of the tool. All credit for the tool's development goes to the original authors.

⁠Usage

⁠Docker

# Pull the latest version
docker pull getwilds/dropletutils:latest

# Or pull a specific version
docker pull getwilds/dropletutils:1.32.0

# Alternatively, pull from GitHub Container Registry
docker pull ghcr.io/getwilds/dropletutils:latest

⁠Singularity/Apptainer

# Pull the latest version
apptainer pull docker://getwilds/dropletutils:latest

# Or pull a specific version
apptainer pull docker://getwilds/dropletutils:1.32.0

# Alternatively, pull from GitHub Container Registry
apptainer pull docker://ghcr.io/getwilds/dropletutils:latest

⁠Example Commands

# Launch an interactive R session with DropletUtils loaded
docker run --rm -it -v /path/to/data:/data getwilds/dropletutils:latest R

# Read a 10x Genomics count matrix and identify real cells vs. empty droplets
docker run --rm -v /path/to/data:/data getwilds/dropletutils:latest \
  Rscript -e "
    library(DropletUtils);
    sce <- read10xCounts('/data/raw_feature_bc_matrix');
    out <- emptyDrops(counts(sce));
    write.csv(as.data.frame(out), '/data/empty_drops_results.csv')
  "

# Run a custom R script that uses DropletUtils
docker run --rm -v /path/to/data:/data getwilds/dropletutils:latest \
  Rscript /data/my_analysis.R

# Alternatively using Apptainer
apptainer run --bind /path/to/data:/data docker://getwilds/dropletutils:latest R

⁠Dockerfile Structure

The Dockerfile follows these main steps:

1. Uses the bioconductor/bioconductor_docker:RELEASE_3_23 base image
2. Adds metadata labels for documentation and attribution
3. Sets R library paths to avoid host contamination in Apptainer
4. Installs DropletUtils via BiocManager::install
5. Runs a smoke test to confirm the package loads correctly
6. Sets a default working directory for data analysis

⁠Security Scanning and CVEs

These images are regularly scanned for vulnerabilities using Docker Scout. However, due to the nature of bioinformatics software and their dependencies, some Docker images may contain components with known vulnerabilities (CVEs).

Use at your own risk: While we strive to minimize security issues, these images are primarily designed for research and analytical workflows in controlled environments.

For the latest security information about this image, please check the CVEs_*.md files in this directory⁠, which are automatically updated through our GitHub Actions workflow. If a particular vulnerability is of concern, please file an issue⁠ in the GitHub repo citing which CVE you would like to be addressed.

⁠Source Repository

These Dockerfiles are maintained in the WILDS Docker Library⁠ repository.