Typical morphological profiling datasets have millions of cells and hundreds of features per cell. When working with this data, you must clean the data, normalize the features to make them comparable across experiments, transform the features, select features based on their quality, and aggregate the single-cell data, if needed. 'cytominer' makes these steps fast and easy. Methods used in practice in the field are discussed in Caicedo (2017) <doi:10.1038/nmeth.4397>. An overview of the field is presented in Caicedo (2016) <doi:10.1016/j.copbio.2016.04.003>.
| Version: | 0.2.2 |
| Depends: | R (≥ 3.3.0) |
| Imports: | caret (≥ 6.0.76), doParallel (≥ 1.0.10), dplyr (≥ 0.8.5), foreach (≥ 1.4.3), futile.logger (≥ 1.4.3), magrittr (≥ 1.5), Matrix (≥ 1.2), purrr (≥ 0.3.3), rlang (≥ 0.4.5), tibble (≥ 2.1.3), tidyr (≥ 1.0.2) |
| Suggests: | DBI (≥ 0.7), dbplyr (≥ 1.4.2), knitr (≥ 1.17), lazyeval (≥ 0.2.0), readr (≥ 1.1.1), rmarkdown (≥ 1.6), RSQLite (≥ 2.0), stringr (≥ 1.2.0), testthat (≥ 1.0.2) |
| Published: | 2020-05-09 |
| Author: | Tim Becker [aut], Allen Goodman [aut], Claire McQuin [aut], Mohammad Rohban [aut], Shantanu Singh [aut, cre] |
| Maintainer: | Shantanu Singh <shsingh at broadinstitute.org> |
| BugReports: | https://github.com/cytomining/cytominer/issues |
| License: | BSD_3_clause + file LICENSE |
| URL: | https://github.com/cytomining/cytominer |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| CRAN checks: | cytominer results |
| Reference manual: | cytominer.pdf |
| Vignettes: |
Introduction to cytominer |
| Package source: | cytominer_0.2.2.tar.gz |
| Windows binaries: | r-devel: cytominer_0.2.2.zip, r-release: cytominer_0.2.2.zip, r-oldrel: cytominer_0.2.2.zip |
| macOS binaries: | r-release: cytominer_0.2.2.tgz, r-oldrel: cytominer_0.2.2.tgz |
| Old sources: | cytominer archive |
Please use the canonical form https://CRAN.R-project.org/package=cytominer to link to this page.