nucim: Nucleome Imaging Toolbox

Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

AuthorVolker Schmid [aut, cre]
Date of publication2016-12-05 21:44:15
MaintainerVolker Schmid <stats@volkerschmid.de>
LicenseGPL-3
Version1.0.0
https://bioimaginggroup.github.io/nucim

View on CRAN

Man pages

barplot_with_interval: Barplot with Intervals

barplot_with_interval_23: Barplot with Intervals for two or three bars beside

classify: Classify DAPI

classify.folder: Classify DAPI

classify.single: Classify DAPI

classify.table: Classify DAPI from class image

class.neighbours: Class neighbourhood distribution

class.neighbours.folder: class.neighbours.folder

colors.in.classes: Compute colors in classes distribution

colors.in.classes.folder: Compute colors in classes distribution for folders

compute.distance2border: Compute distance to border of classes

dapimask: Mask DAPI in kernel

dapimask.file: Automatic DAPI mask segmentation for files

dapimask.folder: Automatic DAPI mask segmentation for folder

find.spots.file: Detects spotsfor one file

find.spots.folder: Detects spots

heatmap7: Heatmap colors for 7 classes

heatmap.color: Heatmap colors for n classes

nearestClassDistances.folder: Find all distances to next neighbour of all classes for...

plot_classify.folder: Plot barplot for classified images in a folder

plot_colors.in.classes.folder: Plot for colors in classes distribution for folders

plot_nearestClassDistances.folder: Plots all distances to next neighbour of all classes for...

splitchannel: Split RGB channels

splitchannels: Split RGB images into channels and pixel size information

splitchannels.file: Split channels into files and extracts size in microns

splitchannels.folder: Split RGB images into channels and pixel size information

spots.combined: Find spots using information from two channels

spots.combined.file: Find spots using information from two channels

spots.combined.folder: Find spots using information from two channels for folder

t_colors.in.classes.folder: Test for colors in classes distribution for folders

Files in this package

nucim
nucim/inst
nucim/inst/doc
nucim/inst/doc/DAPIclassification.html
nucim/inst/doc/DAPIclassification.Rmd
nucim/NAMESPACE
nucim/NEWS
nucim/R
nucim/R/classes.R nucim/R/utils.R nucim/R/spots_combined.R nucim/R/nearest_class_folder.R nucim/R/dapimask.R nucim/R/dapimask_folder.R nucim/R/class_neighbours.R nucim/R/find_spots.R nucim/R/colorsinclasses.R nucim/R/heatmap7.R nucim/R/splitchannels.R nucim/R/t_colors_in_classes_folder.R nucim/R/plot_classify_folder.R nucim/R/dapimask_file.R nucim/R/barplot_with_ci.R nucim/R/splitchannel.R nucim/R/plot_colors_in_classes.R nucim/R/onattach.R nucim/R/plot_nearest_class_folder.R nucim/R/compute_distance2border.R
nucim/vignettes
nucim/vignettes/DAPIclassification.Rmd
nucim/README.md
nucim/MD5
nucim/build
nucim/build/vignette.rds
nucim/DESCRIPTION
nucim/man
nucim/man/t_colors.in.classes.folder.Rd nucim/man/classify.table.Rd nucim/man/splitchannel.Rd nucim/man/heatmap.color.Rd nucim/man/plot_nearestClassDistances.folder.Rd nucim/man/find.spots.file.Rd nucim/man/splitchannels.folder.Rd nucim/man/barplot_with_interval_23.Rd nucim/man/classify.Rd nucim/man/spots.combined.folder.Rd nucim/man/classify.folder.Rd nucim/man/colors.in.classes.folder.Rd nucim/man/nearestClassDistances.folder.Rd nucim/man/class.neighbours.folder.Rd nucim/man/class.neighbours.Rd nucim/man/dapimask.Rd nucim/man/find.spots.folder.Rd nucim/man/splitchannels.file.Rd nucim/man/colors.in.classes.Rd nucim/man/barplot_with_interval.Rd nucim/man/plot_classify.folder.Rd nucim/man/plot_colors.in.classes.folder.Rd nucim/man/compute.distance2border.Rd nucim/man/spots.combined.Rd nucim/man/heatmap7.Rd nucim/man/dapimask.folder.Rd nucim/man/dapimask.file.Rd nucim/man/splitchannels.Rd nucim/man/classify.single.Rd nucim/man/spots.combined.file.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.