nucim: Nucleome Imaging Toolbox
Version 1.0.0

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
URL https://bioimaginggroup.github.io/nucim
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("nucim")

Getting started

README.md
Chromatin compaction classification using DAPI intensity"

Popular man pages

barplot_with_interval: Barplot with Intervals
classify: Classify DAPI
classify.single: Classify DAPI
dapimask: Mask DAPI in kernel
heatmap7: Heatmap colors for 7 classes
heatmap.color: Heatmap colors for n classes
t_colors.in.classes.folder: Test for colors in classes distribution for folders
See all...

All man pages Function index File listing

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 Source code
barplot_with_interval_23 Man page Source code
cfl.helper Source code
class.neighbours Man page Source code
class.neighbours.folder Man page Source code
class.neighbours.one Source code
classify Man page Source code
classify.file Source code
classify.folder Man page Source code
classify.single Man page Source code
classify.table Man page Source code
colors.in.classes Man page Source code
colors.in.classes.files Source code
colors.in.classes.folder Man page Source code
comparefilelist Source code
compute.distance2border Man page Source code
compute.distance2border.nospots.file Source code
compute.distance2border.spots.file Source code
dapimask Man page Source code
dapimask.file Man page Source code
dapimask.folder Man page Source code
find.first.mode Source code
find.mode Source code
find.spots.file Man page Source code
find.spots.folder Man page Source code
heatmap.color Man page Source code
heatmap7 Man page Source code
loadcic Source code
ncd.helper Source code
ncd.helper.min Source code
ncd.helper.qu Source code
nearestClassDistances.files Source code
nearestClassDistances.folder Man page Source code
nucim.chisq.test Source code
nucim.print.p Source code
onAttach Source code
plot_classify.folder Man page Source code
plot_colors.in.classes.folder Man page Source code
plot_nearestClassDistances.folder Man page Source code
read.table.helper Source code
splitchannel Man page Source code
splitchannels Man page Source code
splitchannels.file Man page Source code
splitchannels.folder Man page Source code
spots.combined Man page Source code
spots.combined.file Man page Source code
spots.combined.folder Man page Source code
t_colors.in.classes.folder Man page Source code
thresh.fc Source code

Files

inst
inst/doc
inst/doc/DAPIclassification.html
inst/doc/DAPIclassification.Rmd
NAMESPACE
NEWS
R
R/classes.R
R/utils.R
R/spots_combined.R
R/nearest_class_folder.R
R/dapimask.R
R/dapimask_folder.R
R/class_neighbours.R
R/find_spots.R
R/colorsinclasses.R
R/heatmap7.R
R/splitchannels.R
R/t_colors_in_classes_folder.R
R/plot_classify_folder.R
R/dapimask_file.R
R/barplot_with_ci.R
R/splitchannel.R
R/plot_colors_in_classes.R
R/onattach.R
R/plot_nearest_class_folder.R
R/compute_distance2border.R
vignettes
vignettes/DAPIclassification.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/t_colors.in.classes.folder.Rd
man/classify.table.Rd
man/splitchannel.Rd
man/heatmap.color.Rd
man/plot_nearestClassDistances.folder.Rd
man/find.spots.file.Rd
man/splitchannels.folder.Rd
man/barplot_with_interval_23.Rd
man/classify.Rd
man/spots.combined.folder.Rd
man/classify.folder.Rd
man/colors.in.classes.folder.Rd
man/nearestClassDistances.folder.Rd
man/class.neighbours.folder.Rd
man/class.neighbours.Rd
man/dapimask.Rd
man/find.spots.folder.Rd
man/splitchannels.file.Rd
man/colors.in.classes.Rd
man/barplot_with_interval.Rd
man/plot_classify.folder.Rd
man/plot_colors.in.classes.folder.Rd
man/compute.distance2border.Rd
man/spots.combined.Rd
man/heatmap7.Rd
man/dapimask.folder.Rd
man/dapimask.file.Rd
man/splitchannels.Rd
man/classify.single.Rd
man/spots.combined.file.Rd
nucim documentation built on May 19, 2017, 8:03 a.m.

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

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

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