cytominer: Methods for Image-Based Cell Profiling

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>.

Package details

AuthorTim Becker [aut], Allen Goodman [aut], Claire McQuin [aut], Mohammad Rohban [aut], Shantanu Singh [aut, cre]
MaintainerShantanu Singh <>
LicenseBSD_3_clause + file LICENSE
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:

Try the cytominer package in your browser

Any scripts or data that you put into this service are public.

cytominer documentation built on July 8, 2020, 5:08 p.m.