Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference (original) (raw)

SCdeconR aims to provide a streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential and gene-set enrichment analysis. SCdeconR provides a simulation framework to generate artificial bulk samples for benchmarking purposes. It also provides various visualization options to compare the influence of adjusting for cell-proportions differences on differential expression and pathway analyses.

Installation

To use scaden within SCdeconR, follow the below steps:

Intall scaden python package:

Use pip:

pip install scaden

Or use Conda:

conda install scaden

Then provide your desired python path (that have scaden installed) to option pythonpath for function scdecon. You should be good to go.

The following packages are optional, and only needed for specific methods within SCdeconR.

Usage

See here for detailed documentation and tutorials.

See here for a document to reproduce the results from the study.