MALATin

MALATin is an R package for identifying and filtering low-MALAT1 cells in single-cell RNA-sequencing (scRNA-seq) data. Low MALAT1 expression is associated with cells lacking an intact nucleus, including empty droplets, cell fragments, and mature erythrocytes. The package automatically estimates a data-driven MALAT1 expression threshold using a two-component gamma mixture model and returns the cells that pass this quality-control filter.

This package can be used to extract cells from a raw matrix of cells + empty droplets (e.g. as an alternative to EmptyDrops or CellRanger), or on a filtered matrix of cells but before clustering and differential expression analysis.

For a detailed description of the method, please see our preprint:

Clarke and Bader (2024). MALAT1 expression indicates cell quality in single-cell RNA sequencing data. BioRxiv. https://doi.org/10.1101/2024.07.14.603469.

If you encounter unexpected behaviour or have suggestions for improvements, please open a GitHub issue.

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Installation

Install the development version from GitHub using remotes or devtools:

# install.packages("remotes")
remotes::install_github("BaderLab/malatin")

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Quick start

Filter an existing vector of MALAT1 counts

library(malatin)

data(example_counts)
data(example_barcodes)

# From an object already filtered with e.g. CellRanger or EmptyDrops
result <- malat1_thres_filtered(counts = example_counts, barcodes = example_barcodes)
# From a raw sample that has not yet been processed by e.g. CellRanger or EmptyDrops
# result <- malat1_thres_raw(counts = example_counts, barcodes = example_barcodes)

result$threshold head(result$cells)

The returned object is a list containing

• threshold: estimated MALAT1 threshold
• cells: barcodes of cells passing the filter
• plot: histogram with fitted mixture model (optional)
• histogram: histogram of MALAT1 expression (optional)

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Read CellRanger output directly

For raw Cell Ranger output:

result <- malat1_read_10X_raw(raw_cellranger_folder = "filtered_feature_bc_matrix/")

or from an HDF5 file:

result <- malat1_read_10X_h5_raw(raw_cellranger_h5 = "filtered_feature_bc_matrix.h5")

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Output

The package estimates a minimum MALAT1 expression threshold by fitting a two-component gamma mixture model to the MALAT1 distribution.

Depending on the function arguments, the returned object may include

• the estimated threshold,
• the barcodes of cells passing the filter,
• a histogram of MALAT1 expression,
• the fitted mixture model overlaid on the histogram.

These plots can be used to visually assess whether the inferred threshold is appropriate for your dataset.

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Included example data

Included example data

The package contains a small example dataset:

• example_counts
• example_barcodes

These datasets are used throughout the package examples and can also be used for testing installations.

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Citation

If you use MALATin in your research, please cite:

Clarke and Bader (2024). MALAT1 expression indicates cell quality in single-cell RNA sequencing data. BioRxiv. https://doi.org/10.1101/2024.07.14.603469.

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Issues

If you encounter bugs or have suggestions for improvements, please open a GitHub Issue.

We are happy to help troubleshoot unusual datasets and improve the robustness of the package.