SCdeconR: Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference

Streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential expression and gene-set enrichment analysis. Provide various visualization functions.

Version: 1.0.0
Depends: dplyr, edgeR, foreach, ggplot2, R (≥ 2.10), Seurat
Imports: data.table, gtools, harmony, MASS, Matrix, NMF, reshape2, Biobase, mgcv, grDevices, glmGamPoi
Suggests: FARDEEP, reticulate, plotly, DESeq2, knitr, limma, nnls, preprocessCore, rmarkdown, scater, scran, SingleCellExperiment, doFuture, future, sctransform, Linnorm
Published: 2024-03-22
Author: Yuanhang Liu [aut, cre]
Maintainer: Yuanhang Liu <liu.yuanhang at mayo.edu>
License: GPL (≥ 3)
URL: https://github.com/Liuy12/SCdeconR/, https://liuy12.github.io/SCdeconR/
NeedsCompilation: no
Materials: README NEWS
CRAN checks: SCdeconR results

Documentation:

Reference manual: SCdeconR.pdf

Downloads:

Package source: SCdeconR_1.0.0.tar.gz
Windows binaries: r-prerel: SCdeconR_1.0.0.zip, r-release: SCdeconR_1.0.0.zip, r-oldrel: SCdeconR_1.0.0.zip
macOS binaries: r-prerel (arm64): not available, r-release (arm64): not available, r-oldrel (arm64): not available, r-prerel (x86_64): SCdeconR_1.0.0.tgz, r-release (x86_64): not available

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