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cytominer

Methods for Image-Based Cell Profiling

https://github.com/cytomining/cytominer

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    4 of 9 committers (44.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.9%) to scientific vocabulary

Keywords

microscopy profiling r
Last synced: 4 months ago · JSON representation ·

Repository

Methods for Image-Based Cell Profiling

Basic Info
Statistics
  • Stars: 51
  • Watchers: 6
  • Forks: 28
  • Open Issues: 7
  • Releases: 3
Topics
microscopy profiling r
Created over 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog Contributing License Citation

README.md

Build Status Coverage Status CRAN\_Status\_Badge

cytominer

Typical morphological profiling datasets have millions of cells and hundreds of features per cell. When working with this data, you must

  • clean the data

  • normalize the features so that they are comparable across experiments

  • transform the features so that their distributions are well-behaved ( i.e., bring them in line with assumptions we want to make about their disributions)

  • select features based on their quality

  • aggregate the single-cell data, if needed

The cytominer package makes these steps fast and easy.

Installation

You can install cytominer from CRAN:

r install.packages("cytominer")

Or, install the development version from GitHub:

``` r

install.packages("devtools")

devtools::installgithub("cytomining/cytominer", dependencies = TRUE, buildvignettes = TRUE) ```

Occasionally, the Suggests dependencies may not get installed, depending on your system, so you'd need to install those explicitly.

Example

See vignette("cytominer-pipeline") for basic example of using cytominer to analyze a morphological profiling dataset.

Owner

  • Name: cytomining
  • Login: cytomining
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Singh"
  given-names: "Shantanu"
  orcid: "https://orcid.org/0000-0003-3150-3025"
- family-names: "Goodman"
  given-names: "Allen"
  orcid: "https://orcid.org/0000-0002-6434-2320"
- family-names: "Becker"
  given-names: "Tim"
  orcid: "https://orcid.org/0000-0001-9615-0799"
- family-names: "McQuin"
  given-names: "Claire"
- family-names: "Rohban"
  given-names: "Mohammad H."
  orcid: "https://orcid.org/0000-0001-6589-850X"
- family-names: "Way"
  given-names: "Gregory P."
  orcid: "https://orcid.org/0000-0002-0503-9348"
- family-names: "Cimini"
  given-names: "Beth A."
  orcid: "https://orcid.org/0000-0001-9640-9318"
- family-names: "Carpenter"
  given-names: "Anne E."
  orcid: "https://orcid.org/0000-0003-1555-8261"
title: "Cytominer: Methods for Image-Based Cell Profiling"
version: 0.2.2
date-released: 2020-05-09
url: "https://cran.r-project.org/package=cytominer"

GitHub Events

Total
  • Watch event: 3
Last Year
  • Watch event: 3

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 418
  • Total Committers: 9
  • Avg Commits per committer: 46.444
  • Development Distribution Score (DDS): 0.081
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Shantanu Singh s****h@b****g 384
Mohammad Hossein Rohban m****n@b****g 12
Tim Becker t****r@b****g 7
Shantanu Singh s****h@w****g 7
Allen Goodman a****n@i****m 3
Claire McQuin m****n 2
bethac07 b****7 1
Vincent Rubinetti v****i@g****m 1
Gregory Way g****y@g****m 1
Committer Domains (Top 20 + Academic)
broadinstitute.org: 3 wmc94-e26.broadinstitute.org: 1

Issues and Pull Requests

Last synced: 5 months ago

All Time
  • Total issues: 53
  • Total pull requests: 64
  • Average time to close issues: about 1 year
  • Average time to close pull requests: 9 days
  • Total issue authors: 7
  • Total pull request authors: 6
  • Average comments per issue: 1.38
  • Average comments per pull request: 0.53
  • Merged pull requests: 56
  • 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
View more stats
Top Authors
Issue Authors
  • shntnu (41)
  • mrohban (4)
  • cells2numbers (3)
  • PeterLu0403 (2)
  • hadley (1)
  • gwaybio (1)
  • kvshams (1)
Pull Request Authors
  • shntnu (50)
  • mrohban (9)
  • mcquin (2)
  • sbamin (2)
  • cells2numbers (1)
Top Labels
Issue Labels
feature request (12) question (5) wontfix (5) bug (2)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 292 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 6
  • Total maintainers: 1
proxy.golang.org: github.com/cytomining/cytominer
  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.8%
Last synced: 5 months ago
cran.r-project.org: cytominer

Methods for Image-Based Cell Profiling

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 292 Last month
Rankings
Forks count: 2.7%
Stargazers count: 7.4%
Dependent repos count: 19.3%
Average: 20.2%
Dependent packages count: 28.8%
Downloads: 42.8%
Maintainers (1)
shsingh@broadinstitute.org
Last synced: 5 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.3.0 depends
  • Matrix >= 1.2 imports
  • caret >= 6.0.76 imports
  • doParallel >= 1.0.10 imports
  • dplyr >= 0.8.5 imports
  • foreach >= 1.4.3 imports
  • futile.logger >= 1.4.3 imports
  • glue * imports
  • magrittr >= 1.5 imports
  • purrr >= 0.3.3 imports
  • rlang >= 0.4.5 imports
  • tibble >= 2.1.3 imports
  • tidyr >= 1.0.2 imports
  • DBI >= 0.7 suggests
  • RSQLite >= 2.0 suggests
  • dbplyr >= 1.4.2 suggests
  • knitr >= 1.17 suggests
  • lazyeval >= 0.2.0 suggests
  • readr >= 1.1.1 suggests
  • rmarkdown >= 1.6 suggests
  • stringr >= 1.2.0 suggests
  • testthat >= 1.0.2 suggests