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A library for the statistical deconvolution of RNA bulk samples with single-cell references.

Project description

RNA-Sieve

RNA-Sieve is a method for the deconvolution of bulk cell samples via single-cell RNA expression data.

RNA-sieve-viz

Associated Work

Our preprint is currently available at https://www.biorxiv.org/content/10.1101/2020.10.01.322867v1.

If you find RNA-Sieve useful, please cite our work at:

RNA-Sieve: A likelihood-based deconvolution of bulk gene expression data using single-cell references
<small>Dan D. Erdmann-Pham, Jonathan Fischer, Justin Hong, Yun S. Song
</small> bioRxiv 2020.10.01.322867; doi: https://doi.org/10.1101/2020.10.01.322867

Installation

For Python 3, we recommend that you install rna-sieve via pip.

$ pip3 install rna-sieve

Example Usage

muscle-FD-example

For example usage, please reference the example Jupyter notebook for Python 3 usage, or the Mathematica notebook for Mathematica usage.

The core algorithm is called find_mixtures/findMixtures which takes in a vector of bulk expressions to be deconvolved and reference matrices of means, variances, and sample counts. Currently, only the Python library takes allows for multiple bulks to be jointly deconvolved with a single set of reference matrices.

Project details


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Files for rnasieve, version 0.1.2
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