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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 |
| 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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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.