GitHub - Liuy12/SCdeconR: Deconvolution of bulk RNA-seq data using single-cell RNA-seq data as reference (original) (raw)

SCdeconR

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

install devtools if it's not installed already

if (!require("devtools", quietly = TRUE)) install.packages("devtools") devtools::install_github("liuy12/SCdeconR")

To use scaden within SCdeconR, follow the below steps:

install reticulate package first

install.packages("reticulate")

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.

install BiocManager if it's not installed already

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

data normalization

scater

BiocManager::install("scater")

scran

BiocManager::install("scran")

Linnorm

BiocManager::install("Linnorm")

SingleCellExperiment

BiocManager::install("SingleCellExperiment")

deconvolution methods

FARDEEP

install.packages("FARDEEP")

nnls

install.packages("nnls")

MuSiC

devtools::install_github('xuranw/MuSiC')

SCDC

devtools::install_github("meichendong/SCDC")

differential expression

DESeq2

BiocManager::install("DESeq2")

cell-type specific gene expression

spacexr

devtools::install_github("dmcable/spacexr", build_vignettes = FALSE)

interactive plot

install.packages("plotly")

Usage

See here for detailed documentation and tutorials.

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