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

Functions

barplot_with_interval Man page
barplot_with_interval_23 Man page
classify Man page
classify.folder Man page
classify.single Man page
classify.table Man page
class.neighbours Man page
class.neighbours.folder Man page
colors.in.classes Man page
colors.in.classes.folder Man page
compute.distance2border Man page
dapimask Man page
dapimask.file Man page
dapimask.folder Man page
find.spots.file Man page
find.spots.folder Man page
heatmap7 Man page
heatmap.color Man page
nearestClassDistances.folder Man page
plot_classify.folder Man page
plot_colors.in.classes.folder Man page
plot_nearestClassDistances.folder Man page
splitchannel Man page
splitchannels Man page
splitchannels.file Man page
splitchannels.folder Man page
spots.combined Man page
spots.combined.file Man page
spots.combined.folder Man page
t_colors.in.classes.folder Man page

Files

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.