Package: nucim 1.0.13

Volker Schmid

nucim: Nucleome Imaging Toolbox

Tools for 4D nucleome imaging. Quantitative analysis of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. See Volker J. Schmid, Marion Cremer, Thomas Cremer (2017) <doi:10.1016/j.ymeth.2017.03.013>.

Authors:Volker Schmid [aut, cre]

nucim_1.0.13.tar.gz
nucim_1.0.13.zip(r-4.7)nucim_1.0.13.zip(r-4.6)nucim_1.0.13.zip(r-4.5)
nucim_1.0.13.tgz(r-4.6-any)nucim_1.0.13.tgz(r-4.5-any)
nucim_1.0.13.tar.gz(r-4.7-any)nucim_1.0.13.tar.gz(r-4.6-any)
nucim_1.0.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nucim/json (API)

# Install 'nucim' in R:
install.packages('nucim', repos = c('https://bioimaginggroup.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioimaginggroup/nucim/issues

Pkgdown/docs site:https://bioimaginggroup.github.io

On CRAN:

Conda:

4.48 score 2 stars 9 scripts 472 downloads 30 exports 56 dependencies

Last updated from:d38c7568f1. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK149
source / vignettesOK190
linux-release-x86_64OK143
macos-release-arm64OK143
macos-oldrel-arm64OK157
windows-develOK110
windows-releaseOK96
windows-oldrelOK97
wasm-releaseOK126

Exports:barplot_with_intervalbarplot_with_interval_23class.neighboursclass.neighbours.folderclassifyclassify.folderclassify.singleclassify.tablecolors.in.classescolors.in.classes.foldercompute.distance2borderdapimaskdapimask.filedapimask.folderfind.spots.filefind.spots.folderheatmap.colorheatmap7nearestClassDistances.folderplot_classify.folderplot_colors.in.classes.folderplot_nearestClassDistances.foldersplitchannelsplitchannelssplitchannels.filesplitchannels.folderspots.combinedspots.combined.filespots.combined.foldert_colors.in.classes.folder

Dependencies:abindaskpassbase64encBiocGenericsbioimagetoolsbitopsbslibcachemclicurldigestdotCall64EBImageevaluatefastmapfftwtoolsfieldsfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetshttrjpegjquerylibjsonliteknitrlatticelifecyclelocfitmagrittrmapsmemoisemimeopensslpngR6rappdirsRColorBrewerRcppRCurlrlangrmarkdownsassspamstringistringrsystifftinytexvctrsviridisLitexfunyaml

Chromatin compaction classification using DAPI intensity
Preparation | code to classify one rgb image | code to classify a folder full of rgb images
Rendered fromDAPIclassification.Rmdusingknitr::rmarkdown

Last update: 2020-01-16
Started: 2016-11-02

Workflow on a folder
Preparation | Workflow
Rendered fromworkflow_many.Rmdusingknitr::rmarkdown

Last update: 2020-01-16
Started: 2016-12-08

Workflow for 3D SIM nucleome analysis
Rendered fromworkflow.html.asisusingR.rsp::asis

Last update: 2018-10-09
Started: 2018-10-08

Readme and manuals

Help Manual

Help pageTopics
Barplot with Intervalsbarplot_with_interval
Barplot with Intervals for two or three bars besidebarplot_with_interval_23
Class neighbourhood distributionclass.neighbours
class.neighbours.folderclass.neighbours.folder
Classify DAPIclassify
Classify DAPIclassify.folder
Classify DAPIclassify.single
Count classes in classified imageclassify.table
Compute colors in classes distributioncolors.in.classes
Compute colors in classes distribution for folderscolors.in.classes.folder
Compute distance to border of classescompute.distance2border
Mask DAPI in kerneldapimask
Automatic DAPI mask segmentation for filesdapimask.file
Automatic DAPI mask segmentation for folderdapimask.folder
Detects spots for one filefind.spots.file
Detects spotsfind.spots.folder
Heatmap colors for n classesheatmap.color
Heatmap colors for 7 classesheatmap7
Find all distances to next neighbour of all classes for foldersnearestClassDistances.folder
Plot barplot for classified images in a folderplot_classify.folder
Plot for colors in classes distribution for foldersplot_colors.in.classes.folder
Plots all distances to next neighbour of all classes for foldersplot_nearestClassDistances.folder
Split RGB channelssplitchannel
Split RGB images into channels and pixel size informationsplitchannels
Split channels into files and extracts size in micronssplitchannels.file
Split RGB images into channels and pixel size informationsplitchannels.folder
Find spots using information from two channelsspots.combined
Find spots using information from two channelsspots.combined.file
Find spots using information from two channels for folderspots.combined.folder
Test for colors in classes distribution for folderst_colors.in.classes.folder