flowcatchR

Package: flowcatchR
Type: Package
Title: Tools to analyze in vivo microscopy imaging data focused on
tracking flowing blood cells
Version: 1.6.2
Date: 2015-10-08
Authors@R: person("Federico", "Marini", email = "marinif@uni-mainz.de",
role = c("aut", "cre"))
Maintainer: Federico Marini <marinif@uni-mainz.de>
Description: flowcatchR is a set of tools to analyze in vivo microscopy imaging
data, focused on tracking flowing blood cells. It guides the steps from
segmentation to calculation of features, filtering out particles not of
interest, providing also a set of utilities to help checking the quality of
the performed operations (e.g. how good the segmentation was). It allows investigating the
issue of tracking flowing cells such as in blood vessels, to categorize the particles in
flowing, rolling and adherent. This classification is applied in the study of phenomena such as
hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated
workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is
delivered alongside the package, and can enable fully reproducible bioimage analysis in the
R environment.
License: BSD_3_clause + file LICENSE
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, shiny
Depends: R (>= 2.10), methods, EBImage
Imports: rgl, colorRamps, abind, BiocParallel
SystemRequirements: ImageMagick
LazyData: true
URL: https://github.com/federicomarini/flowcatchR
BugReports: https://github.com/federicomarini/flowcatchR/issues
biocViews: Software, Visualization, CellBiology, Classification,
Infrastructure, GUI
NeedsCompilation: no
Packaged: 2016-05-16 04:56:52 UTC; biocbuild
Author: Federico Marini [aut, cre]

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'flowcatchR' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'flowcatchR'
    finding HTML links ... done
    Frames-class                            html  
    Frames                                  html  
    KinematicsFeatures-class                html  
    KinematicsFeaturesSet-class             html  
    LinkedParticleSet-class                 html  
    MesenteriumSubset                       html  
    ParticleSet-class                       html  
    TrajectorySet-class                     html  
    add.contours                            html  
    addParticles                            html  
    axesInfo                                html  
    candidate.platelets                     html  
    channel.Frames                          html  
    computeMSD                              html  
    crop.Frames                             html  
    finding level-2 HTML links ... done

    export.Frames                           html  
    export.particles                        html  
    extractKinematics.traj                  html  
    flowcatchR                              html  
    initialize.LinkedParticleSet            html  
    inspect.Frames                          html  
    kinematics                              html  
    length.Frames                           html  
    link.particles                          html  
    matchTrajToParticles                    html  
    normalizeFrames                         html  
    particles                               html  
    penaltyFunctionGenerator                html  
    plot.TrajectorySet                      html  
    plot2D.TrajectorySet                    html  
    preprocess.Frames                       html  
    read.Frames                             html  
    read.particles                          html  
    repmat                                  html  
    rotate.Frames                           html  
    select.Frames                           html  
    select.particles                        html  
    shinyFlow                               html  
    show-Frames-method                      html  
    show-KinematicsFeatures-method          html  
    show-KinematicsFeaturesSet-method       html  
    show-LinkedParticleSet-method           html  
    show-ParticleSet-method                 html  
    show-TrajectorySet-method               html  
    snap                                    html  
    toCartesianCoords                       html  
    toPolarCoords                           html  
    trajectories                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowcatchR)
Making 'packages.html' ... done