BisqueRNA: Decomposition of Bulk Expression with Single-Cell Sequencing

Provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples. For more details, see Jew and Alvarez et al (2019) <doi:10.1101/669911>.

Version: 1.0
Depends: R (≥ 3.5.0)
Imports: Biobase, lsei, methods, stats
Suggests: Seurat, plyr, knitr, rmarkdown, testthat
Published: 2019-06-19
Author: Brandon Jew [aut, cre], Marcus Alvarez [aut]
Maintainer: Brandon Jew <brandon.jew at ucla.edu>
BugReports: https://github.com/cozygene/bisque/issues
License: GPL-3
URL: https://www.biorxiv.org/content/10.1101/669911v1
NeedsCompilation: no
Materials: README
CRAN checks: BisqueRNA results

Downloads:

Reference manual: BisqueRNA.pdf
Vignettes: Bisque Example Usage
Package source: BisqueRNA_1.0.tar.gz
Windows binaries: r-devel: BisqueRNA_1.0.zip, r-release: BisqueRNA_1.0.zip, r-oldrel: BisqueRNA_1.0.zip
OS X binaries: r-release: BisqueRNA_1.0.tgz, r-oldrel: BisqueRNA_1.0.tgz

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