Science Score: 44.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (8.4%) to scientific vocabulary
Last synced: 9 months ago
·
JSON representation
·
Repository
Shiny App for CPTrackR
Basic Info
- Host: GitHub
- Owner: burgerga
- License: other
- Language: R
- Default Branch: main
- Size: 98.6 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Created over 5 years ago
· Last pushed over 2 years ago
Metadata Files
Readme
Changelog
License
Citation
README.Rmd
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# CPTrackRApp
[](https://www.tidyverse.org/lifecycle/#experimental)
## Overview
The goal of CPTrackRApp is to [fix track identifiers](https://forum.image.sc/t/tracking-label/16409) from [CellProfiler](https://cellprofiler.org/)'s sqlite output. CPTrackRApp is a Shiny app that analyses the sqlite file, and determines the parameters for [CPTrackR](https://github.com/burgerga/CPTrackR) to fix the track.
Additionally it shows the CellProfiler pipeline metadata, and previews the fixed tracks.
## Installation
You can install the development version of CPTrackRApp from with:
```{r, eval=F}
# install.packages("remotes")
remotes::install_github("burgerga/CPTrackRApp")
```
## Usage
To start the app use
```{r, eval=F}
CPTrackRApp::run_app()
```
**Screenshot:**
Owner
- Name: Gerhard Burger
- Login: burgerga
- Kind: user
- Location: Gouda
- Company: Leiden University
- Website: https://www.universiteitleiden.nl/en/staffmembers/gerhard-burger
- Repositories: 8
- Profile: https://github.com/burgerga
Assistant Professor / Open Source Enthusiast
Citation (CITATION.cff)
# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.5.0
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
cff-version: 1.2.0
message: 'To cite package "CPTrackRApp" in publications use:'
type: software
license: MIT
title: 'CPTrackRApp: CPTrackR App'
version: 0.0.0.9003
abstract: An app to explore CellProfiler tracking output.
authors:
- family-names: Burger
given-names: Gerhard
email: burger.ga@gmail.com
orcid: https://orcid.org/0000-0003-1062-5576
repository-code: https://github.com/burgerga/CPTrackRApp
url: https://github.com/burgerga/CPTrackRApp
contact:
- family-names: Burger
given-names: Gerhard
email: burger.ga@gmail.com
orcid: https://orcid.org/0000-0003-1062-5576
references:
- type: software
title: config
abstract: 'config: Manage Environment Specific Configuration Values'
notes: Imports
url: https://rstudio.github.io/config/
repository: https://CRAN.R-project.org/package=config
authors:
- family-names: Allaire
given-names: JJ
email: jj@rstudio.com
year: '2023'
- type: software
title: golem
abstract: 'golem: A Framework for Robust Shiny Applications'
notes: Imports
url: https://github.com/ThinkR-open/golem
repository: https://CRAN.R-project.org/package=golem
authors:
- family-names: Fay
given-names: Colin
email: contact@colinfay.me
orcid: https://orcid.org/0000-0001-7343-1846
- family-names: Guyader
given-names: Vincent
email: vincent@thinkr.fr
orcid: https://orcid.org/0000-0003-0671-9270
- family-names: Rochette
given-names: Sébastien
email: sebastien@thinkr.fr
orcid: https://orcid.org/0000-0002-1565-9313
- family-names: Girard
given-names: Cervan
email: cervan@thinkr.fr
orcid: https://orcid.org/0000-0002-4816-4624
year: '2023'
- type: software
title: shiny
abstract: 'shiny: Web Application Framework for R'
notes: Imports
url: https://shiny.posit.co/
repository: https://CRAN.R-project.org/package=shiny
authors:
- family-names: Chang
given-names: Winston
email: winston@posit.co
orcid: https://orcid.org/0000-0002-1576-2126
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Allaire
given-names: JJ
email: jj@posit.co
- family-names: Sievert
given-names: Carson
email: carson@posit.co
orcid: https://orcid.org/0000-0002-4958-2844
- family-names: Schloerke
given-names: Barret
email: barret@posit.co
orcid: https://orcid.org/0000-0001-9986-114X
- family-names: Xie
given-names: Yihui
email: yihui@posit.co
- family-names: Allen
given-names: Jeff
- family-names: McPherson
given-names: Jonathan
email: jonathan@posit.co
- family-names: Dipert
given-names: Alan
- family-names: Borges
given-names: Barbara
year: '2023'
- type: software
title: processx
abstract: 'processx: Execute and Control System Processes'
notes: Imports
url: https://processx.r-lib.org
repository: https://CRAN.R-project.org/package=processx
authors:
- family-names: Csárdi
given-names: Gábor
email: csardi.gabor@gmail.com
orcid: https://orcid.org/0000-0001-7098-9676
- family-names: Chang
given-names: Winston
year: '2023'
- type: software
title: attempt
abstract: 'attempt: Tools for Defensive Programming'
notes: Imports
url: https://github.com/ColinFay/attempt
repository: https://CRAN.R-project.org/package=attempt
authors:
- family-names: Fay
given-names: Colin
email: contact@colinfay.me
orcid: https://orcid.org/0000-0001-7343-1846
year: '2023'
- type: software
title: DT
abstract: 'DT: A Wrapper of the JavaScript Library ''DataTables'''
notes: Imports
url: https://github.com/rstudio/DT
repository: https://CRAN.R-project.org/package=DT
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
- family-names: Cheng
given-names: Joe
- family-names: Tan
given-names: Xianying
year: '2023'
- type: software
title: glue
abstract: 'glue: Interpreted String Literals'
notes: Imports
url: https://glue.tidyverse.org/
repository: https://CRAN.R-project.org/package=glue
authors:
- family-names: Hester
given-names: Jim
orcid: https://orcid.org/0000-0002-2739-7082
- family-names: Bryan
given-names: Jennifer
email: jenny@rstudio.com
orcid: https://orcid.org/0000-0002-6983-2759
year: '2023'
- type: software
title: htmltools
abstract: 'htmltools: Tools for HTML'
notes: Imports
url: https://rstudio.github.io/htmltools/
repository: https://CRAN.R-project.org/package=htmltools
authors:
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Sievert
given-names: Carson
email: carson@posit.co
orcid: https://orcid.org/0000-0002-4958-2844
- family-names: Schloerke
given-names: Barret
email: barret@posit.co
orcid: https://orcid.org/0000-0001-9986-114X
- family-names: Chang
given-names: Winston
email: winston@posit.co
orcid: https://orcid.org/0000-0002-1576-2126
- family-names: Xie
given-names: Yihui
email: yihui@posit.co
- family-names: Allen
given-names: Jeff
year: '2023'
- type: software
title: CPTrackR
abstract: 'CPTrackR: Create unique track identifiers for CellProfiler tracking output'
notes: Imports
authors:
- family-names: Burger
given-names: Gerhard
email: burger.ga@gmail.com
orcid: https://orcid.org/0000-0003-1062-5576
- family-names: Heldring
given-names: Muriel
email: murielheldring@gmail.com
orcid: https://orcid.org/0000-0002-3565-7227
- family-names: Wink
given-names: Steven
email: hardervidertsie@gmail.com
orcid: https://orcid.org/0000-0003-1189-7231
version: '>= 0.2.2'
year: '2023'
- type: software
title: celltrackR
abstract: 'celltrackR: Motion Trajectory Analysis'
notes: Imports
url: http://www.motilitylab.net
repository: https://CRAN.R-project.org/package=celltrackR
authors:
- family-names: Textor
given-names: Johannes
email: johannes.textor@gmx.de
- family-names: Dannenberg
given-names: Katharina
- family-names: Berry
given-names: Jeffrey
- family-names: Burger
given-names: Gerhard
- family-names: Liu
given-names: Annie
- family-names: Wortel
given-names: Inge
email: ingewortel@gmail.com
year: '2023'
- type: software
title: DBI
abstract: 'DBI: R Database Interface'
notes: Imports
url: https://dbi.r-dbi.org
repository: https://CRAN.R-project.org/package=DBI
authors:
- name: R Special Interest Group on Databases (R-SIG-DB)
- family-names: Wickham
given-names: Hadley
- family-names: Müller
given-names: Kirill
email: krlmlr+r@mailbox.org
orcid: https://orcid.org/0000-0002-1416-3412
year: '2023'
- type: software
title: RSQLite
abstract: 'RSQLite: SQLite Interface for R'
notes: Imports
url: https://rsqlite.r-dbi.org
repository: https://CRAN.R-project.org/package=RSQLite
authors:
- family-names: Müller
given-names: Kirill
email: kirill@cynkra.com
orcid: https://orcid.org/0000-0002-1416-3412
- family-names: Wickham
given-names: Hadley
- family-names: James
given-names: David A.
- family-names: Falcon
given-names: Seth
year: '2023'
- type: software
title: pool
abstract: 'pool: Object Pooling'
notes: Imports
url: http://rstudio.github.io/pool/
repository: https://CRAN.R-project.org/package=pool
authors:
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Borges
given-names: Barbara
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2023'
- type: software
title: pkgload
abstract: 'pkgload: Simulate Package Installation and Attach'
notes: Imports
url: https://pkgload.r-lib.org
repository: https://CRAN.R-project.org/package=pkgload
authors:
- family-names: Wickham
given-names: Hadley
- family-names: Chang
given-names: Winston
- family-names: Hester
given-names: Jim
- family-names: Henry
given-names: Lionel
email: lionel@posit.co
year: '2023'
- type: software
title: magrittr
abstract: 'magrittr: A Forward-Pipe Operator for R'
notes: Imports
url: https://magrittr.tidyverse.org
repository: https://CRAN.R-project.org/package=magrittr
authors:
- family-names: Bache
given-names: Stefan Milton
email: stefan@stefanbache.dk
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
year: '2023'
- type: software
title: dplyr
abstract: 'dplyr: A Grammar of Data Manipulation'
notes: Imports
url: https://dplyr.tidyverse.org
repository: https://CRAN.R-project.org/package=dplyr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
orcid: https://orcid.org/0000-0003-4757-117X
- family-names: François
given-names: Romain
orcid: https://orcid.org/0000-0002-2444-4226
- family-names: Henry
given-names: Lionel
- family-names: Müller
given-names: Kirill
orcid: https://orcid.org/0000-0002-1416-3412
- family-names: Vaughan
given-names: Davis
email: davis@posit.co
orcid: https://orcid.org/0000-0003-4777-038X
year: '2023'
- type: software
title: stringr
abstract: 'stringr: Simple, Consistent Wrappers for Common String Operations'
notes: Imports
url: https://stringr.tidyverse.org
repository: https://CRAN.R-project.org/package=stringr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2023'
- type: software
title: stringi
abstract: 'stringi: Fast and Portable Character String Processing Facilities'
notes: Imports
url: https://stringi.gagolewski.com/
repository: https://CRAN.R-project.org/package=stringi
authors:
- family-names: Gagolewski
given-names: Marek
- family-names: Tartanus
given-names: Bartek
- family-names: Unicode
given-names: others;
- name: Inc.
- name: others
year: '2023'
- type: software
title: purrr
abstract: 'purrr: Functional Programming Tools'
notes: Imports
url: https://purrr.tidyverse.org/
repository: https://CRAN.R-project.org/package=purrr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
orcid: https://orcid.org/0000-0003-4757-117X
- family-names: Henry
given-names: Lionel
email: lionel@rstudio.com
year: '2023'
- type: software
title: tibble
abstract: 'tibble: Simple Data Frames'
notes: Imports
url: https://tibble.tidyverse.org/
repository: https://CRAN.R-project.org/package=tibble
authors:
- family-names: Müller
given-names: Kirill
email: kirill@cynkra.com
orcid: https://orcid.org/0000-0002-1416-3412
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
year: '2023'
- type: software
title: dbplyr
abstract: 'dbplyr: A ''dplyr'' Back End for Databases'
notes: Imports
url: https://dbplyr.tidyverse.org/
repository: https://CRAN.R-project.org/package=dbplyr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@rstudio.com
- family-names: Girlich
given-names: Maximilian
- family-names: Ruiz
given-names: Edgar
year: '2023'
version: '>= 2.0.0'
- type: software
title: ggplot2
abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
notes: Imports
url: https://ggplot2.tidyverse.org
repository: https://CRAN.R-project.org/package=ggplot2
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
orcid: https://orcid.org/0000-0003-4757-117X
- family-names: Chang
given-names: Winston
orcid: https://orcid.org/0000-0002-1576-2126
- family-names: Henry
given-names: Lionel
- family-names: Pedersen
given-names: Thomas Lin
email: thomas.pedersen@posit.co
orcid: https://orcid.org/0000-0002-5147-4711
- family-names: Takahashi
given-names: Kohske
- family-names: Wilke
given-names: Claus
orcid: https://orcid.org/0000-0002-7470-9261
- family-names: Woo
given-names: Kara
orcid: https://orcid.org/0000-0002-5125-4188
- family-names: Yutani
given-names: Hiroaki
orcid: https://orcid.org/0000-0002-3385-7233
- family-names: Dunnington
given-names: Dewey
orcid: https://orcid.org/0000-0002-9415-4582
year: '2023'
- type: software
title: shinycssloaders
abstract: 'shinycssloaders: Add Loading Animations to a ''shiny'' Output While It''s
Recalculating'
notes: Imports
url: https://github.com/daattali/shinycssloaders
repository: https://CRAN.R-project.org/package=shinycssloaders
authors:
- family-names: Sali
given-names: Andras
email: andras.sali@alphacruncher.hu
- family-names: Attali
given-names: Dean
email: daattali@gmail.com
year: '2023'
- type: software
title: jsonlite
abstract: 'jsonlite: A Simple and Robust JSON Parser and Generator for R'
notes: Imports
url: https://jeroen.r-universe.dev/jsonlite
repository: https://CRAN.R-project.org/package=jsonlite
authors:
- family-names: Ooms
given-names: Jeroen
email: jeroen@berkeley.edu
orcid: https://orcid.org/0000-0002-4035-0289
year: '2023'
- type: software
title: progressr
abstract: 'progressr: An Inclusive, Unifying API for Progress Updates'
notes: Imports
url: https://progressr.futureverse.org
repository: https://CRAN.R-project.org/package=progressr
authors:
- family-names: Bengtsson
given-names: Henrik
email: henrikb@braju.com
year: '2023'
- type: software
title: mdftracks
abstract: 'mdftracks: Read and Write ''MTrackJ Data Files'''
notes: Imports
url: https://github.com/burgerga/mdftracks
repository: https://CRAN.R-project.org/package=mdftracks
authors:
- family-names: Burger
given-names: Gerhard
email: burger.ga@gmail.com
orcid: https://orcid.org/0000-0003-1062-5576
year: '2023'
- type: software
title: future
abstract: 'future: Unified Parallel and Distributed Processing in R for Everyone'
notes: Imports
url: https://future.futureverse.org
repository: https://CRAN.R-project.org/package=future
authors:
- family-names: Bengtsson
given-names: Henrik
email: henrikb@braju.com
year: '2023'
- type: software
title: tidyr
abstract: 'tidyr: Tidy Messy Data'
notes: Imports
url: https://tidyr.tidyverse.org
repository: https://CRAN.R-project.org/package=tidyr
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Vaughan
given-names: Davis
email: davis@posit.co
- family-names: Girlich
given-names: Maximilian
year: '2023'
- type: software
title: testthat
abstract: 'testthat: Unit Testing for R'
notes: Suggests
url: https://testthat.r-lib.org
repository: https://CRAN.R-project.org/package=testthat
authors:
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
year: '2023'
- type: software
title: knitr
abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
notes: Suggests
url: https://yihui.org/knitr/
repository: https://CRAN.R-project.org/package=knitr
authors:
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
year: '2023'
- type: software
title: rmarkdown
abstract: 'rmarkdown: Dynamic Documents for R'
notes: Suggests
url: https://pkgs.rstudio.com/rmarkdown/
repository: https://CRAN.R-project.org/package=rmarkdown
authors:
- family-names: Allaire
given-names: JJ
email: jj@posit.co
- family-names: Xie
given-names: Yihui
email: xie@yihui.name
orcid: https://orcid.org/0000-0003-0645-5666
- family-names: Dervieux
given-names: Christophe
email: cderv@posit.co
orcid: https://orcid.org/0000-0003-4474-2498
- family-names: McPherson
given-names: Jonathan
email: jonathan@posit.co
- family-names: Luraschi
given-names: Javier
- family-names: Ushey
given-names: Kevin
email: kevin@posit.co
- family-names: Atkins
given-names: Aron
email: aron@posit.co
- family-names: Wickham
given-names: Hadley
email: hadley@posit.co
- family-names: Cheng
given-names: Joe
email: joe@posit.co
- family-names: Chang
given-names: Winston
email: winston@posit.co
- family-names: Iannone
given-names: Richard
email: rich@posit.co
orcid: https://orcid.org/0000-0003-3925-190X
year: '2023'
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
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Dependencies
DESCRIPTION
cran
- CPTrackR >= 0.2.2 imports
- DBI * imports
- DT * imports
- RSQLite * imports
- attempt * imports
- celltrackR * imports
- config * imports
- dbplyr >= 2.0.0 imports
- dplyr * imports
- future * imports
- ggplot2 * imports
- glue * imports
- golem * imports
- htmltools * imports
- jsonlite * imports
- magrittr * imports
- mdftracks * imports
- pkgload * imports
- pool * imports
- processx * imports
- progressr * imports
- purrr * imports
- shiny * imports
- shinycssloaders * imports
- stringi * imports
- stringr * imports
- tibble * imports
- tidyr * imports
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
Dockerfile
docker
- rocker/tidyverse 4.1.2 build