Package: CRImage 1.55.0

Henrik Failmezger

CRImage: CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

Authors:Henrik Failmezger <[email protected]>, Yinyin Yuan <[email protected]>, Oscar Rueda <[email protected]>, Florian Markowetz <[email protected]>

CRImage_1.55.0.tar.gz
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CRImage.pdf |CRImage.html✨
CRImage/json (API)

# Install 'CRImage' in R:

install.packages('CRImage', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:CRImage-1.55.0(bioc 3.21)CRImage-1.54.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cellbiology classification

4.00 score 6 scripts 324 downloads 5 mentions 17 exports 54 dependencies

Last updated 4 months agofrom:181767bd23. Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 19 2025
R-4.5-win	NOTE	Feb 19 2025
R-4.5-mac	NOTE	Feb 19 2025
R-4.5-linux	NOTE	Feb 19 2025
R-4.4-win	NOTE	Feb 19 2025
R-4.4-mac	NOTE	Feb 19 2025
R-4.3-win	NOTE	Feb 19 2025
R-4.3-mac	NOTE	Feb 19 2025

Exports:calculateCellularity calculateMeanStdTarget calculateOtsu classifyCells colorCorrection convertHSVToRGB convertLABToRGB convertRGBToHSV convertRGBToLAB correctCopyNumber createBinaryImage createClassifier labelCells plotCorrectedCN processAperio SauvolaThreshold segmentImage

Dependencies:abind aCGH base64enc Biobase BiocGenerics bitops bslib cachem class cli cluster codetools digest DNAcopy e1071 EBImage evaluate fastmap fftwtools fontawesome foreach fs generics glue highr htmltools htmlwidgets iterators jpeg jquerylib jsonlite knitr lattice lifecycle locfit MASS Matrix memoise mime multtest png proxy R6 rappdirs RCurl rlang rmarkdown sass sgeostat survival tiff tinytex xfun yaml

CRImage Manual

Rendered fromCRImage.Rnwusingutils::Sweaveon Feb 19 2025.

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CRImage is a package to analyze images and classify cells.	CRImage-package CRImage
Calculation of tumour cellularity	calculateCellularity
Calculates Mean and Standard deviation of an image	calculateMeanStdTarget
Does Otsu thresholding	calculateOtsu
A function to classify cells	classifyCells
Color transfer between images.	colorCorrection
Conversion from HSV color space to RGB color space	convertHSVToRGB
Conversion of LAB colour space to RGB colour space	convertLABToRGB
Conversion from RGB color space to HSV color space	convertRGBToHSV
Converts RGB to LAB color space.	convertRGBToLAB
Allelic Copy Number correction for cellularity	correctCopyNumber
Thresholding	createBinaryImage
Construction of a classifier	createClassifier
Interactive Session for cell labeling	labelCells
Plot CN profiles corrected for cellularity	plotCorrectedCN
Cellularity Calculation of Aperio TX Scanner	processAperio
Do Sauvola thresholding	SauvolaThreshold
Segmentation of an image	segmentImage