rcell2: Yeast Cell Cytometry Suite for CellID in R.
In darksideoftheshmoo/rcell2: CellID Data Analysis Inside the Tidyverse
rcell2 R Documentation
Yeast Cell Cytometry Suite for CellID in R.
Description
It is a rewrite and revamp of the previously awesome Rcell package, by Dr. Alan Bush.
Plotting functions from that package have been excluded in the name of minimalism.
Thoughfully, ggplot2 definitions for all those "cplots" are available in our vignettes (happy copy-pasting!).
Details
The full rcell2 functionality is split into three main packages:
rcell2, rcell2.cellid, and rcell2.magick.
rcell2 (tidyCell) functions
The tidyCell functions manage CellID's output.
It includes functions to load individual cell masks from CellID's identified masks, from generated TSV and/or TIFF files (ijtiff is required for the latter).
Also useful to turn custom data into compatible dataframes for the other functions in this package.
rcell2.magick functions
magickCell renders images from individual cells, based on original images, user defined filters and data from cells.
It requires appropriate data frames for observation data (cdata) and for image metadata (paths). It should not be required that the data comes from images processed by CellID.
It relies heavily on the magick package, so the equirement of the imagemagick system library might be inconvenient. That is why this awesome feature is optional.
shinyCell is an R-Shiny based graphical interface, meant to filter, inspect and annotate cells relying on 2D plots of arbitrary variables.
It should not be required that the data comes from images processed by CellID, just as magickCell.
It relies heavily on the magick package, so the equirement of the imagemagick system library might be inconvenient. That is why this awesome feature is optional.
Also included are two apps: tagCell for annotation, and plotApp for plotting and subsetting.
rcell2.cellid functions
This package includes CellID's source code (written in C). During installation, it compiles a binary executable for Linux, Windows, and Mac systems.
The executable is then wrapped seamlessly by the cell2 function, such that CellID can now be used programatically within R.
If you already have CellID in your system, you are welcome to use it instead of the bundled executable.
See Also
ijtiff magick shiny
darksideoftheshmoo/rcell2 documentation built on Oct. 23, 2024, 12:59 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| rcell2 | R Documentation |
Yeast Cell Cytometry Suite for CellID in R.
Description
It is a rewrite and revamp of the previously awesome Rcell package, by Dr. Alan Bush.
Plotting functions from that package have been excluded in the name of minimalism.
Thoughfully, ggplot2 definitions for all those "cplots" are available in our vignettes (happy copy-pasting!).
Details
The full rcell2 functionality is split into three main packages:
rcell2, rcell2.cellid, and rcell2.magick.
rcell2 (tidyCell) functions
The tidyCell functions manage CellID's output. It includes functions to load individual cell masks from CellID's identified masks, from generated TSV and/or TIFF files (ijtiff is required for the latter). Also useful to turn custom data into compatible dataframes for the other functions in this package.
rcell2.magick functions
magickCell renders images from individual cells, based on original images, user defined filters and data from cells.
It requires appropriate data frames for observation data (cdata) and for image metadata (paths). It should not be required that the data comes from images processed by CellID.
It relies heavily on the magick package, so the equirement of the imagemagick system library might be inconvenient. That is why this awesome feature is optional.
shinyCell is an R-Shiny based graphical interface, meant to filter, inspect and annotate cells relying on 2D plots of arbitrary variables.
It should not be required that the data comes from images processed by CellID, just as magickCell.
It relies heavily on the magick package, so the equirement of the imagemagick system library might be inconvenient. That is why this awesome feature is optional.
Also included are two apps: tagCell for annotation, and plotApp for plotting and subsetting.
rcell2.cellid functions
This package includes CellID's source code (written in C). During installation, it compiles a binary executable for Linux, Windows, and Mac systems.
The executable is then wrapped seamlessly by the cell2 function, such that CellID can now be used programatically within R.
If you already have CellID in your system, you are welcome to use it instead of the bundled executable.
See Also
ijtiff magick shiny
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.