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: | 1.0.5 |
Depends: | R (≥ 3.5.0) |
Imports: | Biobase, limSolve, methods, stats |
Suggests: | Seurat, plyr, knitr, rmarkdown, testthat |
Published: | 2021-05-23 |
DOI: | 10.32614/CRAN.package.BisqueRNA |
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 |
In views: | Omics |
CRAN checks: | BisqueRNA results |
Reference manual: | BisqueRNA.pdf |
Vignettes: |
Bisque Example Usage |
Package source: | BisqueRNA_1.0.5.tar.gz |
Windows binaries: | r-devel: BisqueRNA_1.0.5.zip, r-release: BisqueRNA_1.0.5.zip, r-oldrel: BisqueRNA_1.0.5.zip |
macOS binaries: | r-release (arm64): BisqueRNA_1.0.5.tgz, r-oldrel (arm64): BisqueRNA_1.0.5.tgz, r-release (x86_64): BisqueRNA_1.0.5.tgz, r-oldrel (x86_64): BisqueRNA_1.0.5.tgz |
Old sources: | BisqueRNA archive |
Reverse suggests: | lute, mastR |
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