https://github.com/cytomining/cytominer

Methods for Image-Based Cell Profiling
https://github.com/cytomining/cytominer

microscopy profiling r

Last synced: about 2 months ago
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Methods for Image-Based Cell Profiling

• Host: GitHub
• URL: https://github.com/cytomining/cytominer
• Owner: cytomining
• License: other
• Created: 2015-07-20T22:38:45.000Z (almost 9 years ago)
• Default Branch: master
• Last Pushed: 2023-06-29T20:02:36.000Z (about 1 year ago)
• Last Synced: 2024-05-03T15:19:59.260Z (about 2 months ago)
• Topics: microscopy, profiling, r
• Language: R
• Homepage: https://cytomining.github.io/cytominer/
• Size: 235 MB
• Stars: 45
• Watchers: 7
• Forks: 28
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Citation: CITATION.cff

Lists

• awesome-cytodata - Cytominer - Methods for image-based cell profiling in R. (Software / Genetic Perturbations)

README

        
[![Build Status](https://travis-ci.org/cytomining/cytominer.png?branch=master)](https://travis-ci.org/cytomining/cytominer) [![Coverage Status](https://img.shields.io/codecov/c/github/cytomining/cytominer/master.svg)](https://codecov.io/github/cytomining/cytominer?branch=master) [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/cytominer)](https://cran.r-project.org/package=cytominer)



cytominer

=========

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 so that they are comparable across experiments

-   transform the features so that their distributions are well-behaved ( i.e., bring them in line with assumptions we want to make about their disributions)

-   select features based on their quality

-   aggregate the single-cell data, if needed

The cytominer package makes these steps fast and easy.

Installation

------------

You can install `cytominer` from CRAN:

``` r

install.packages("cytominer")

```

Or, install the development version from GitHub:

``` r

# install.packages("devtools")

devtools::install_github("cytomining/cytominer", dependencies = TRUE, build_vignettes = TRUE)

```

Occasionally, the `Suggests` dependencies [may not get installed](https://github.com/hadley/devtools/issues/1370), depending on your system, so you'd need to install those explicitly.

Example

-------

See `vignette("cytominer-pipeline")` for basic example of using cytominer to analyze a morphological profiling dataset.