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ceas

Cellular Energetics Analysis Software

https://github.com/jamespeapen/ceas

Science Score: 57.0%

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
    Found 4 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (18.3%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Cellular Energetics Analysis Software

Basic Info
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 5
Created almost 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License Citation

README.md

ceas

Cellular Energetics Analysis Software

DOI

CRAN release downloads R-CMD-check <!-- badges: end -->

Description

Measuring cellular energetics is essential to understanding a matrix’s (e.g. cell, tissue or biofluid) metabolic state. The Agilent Seahorse machine is a common method to measure real-time cellular energetics, but existing analysis tools are highly manual or lack functionality. The Cellular Energetics Analysis Software (ceas) R package fills this analytical gap by providing modular and automated Seahorse data analysis and visualization using the methods described by Mookerjee et al. (2017).

Pronunciation

'ceas' is pronounced like the word 'seas' (siːz, SEEZ).

Installation

CRAN

r install.packages("ceas")

Github

You can install the release or development versions from GitHub by cloning the repo. The code on the main branch is in sync with the CRAN releases while the dev branch has the latest updates. Documentation for the dev branch can be found on the dev page of the website (/dev).

bash git clone https://github.com/jamespeapen/ceas/ git clone -b dev https://github.com/jamespeapen/ceas/ # dev version R CMD INSTALL ceas

You can also use the R devtools package:

r devtools::install_github("jamespeapen/ceas") devtools::install_github("jamespeapen/ceas", ref = "dev") # dev version

or pak:

r pak::pkg_install("jamespeapen/ceas") pak::pkg_install("jamespeapen/ceas@dev") # dev version

Usage

A user guide is available on the package website. Bug reports may be submitted through GitHub issues.

Citation

If you use ceas please cite

Rachel (Rae) J House, James P Eapen, Hui Shen, Carrie R Graveel, Matthew R Steensma (2024). ceas: An R package for Seahorse data analysis and visualization, Bioinformatics, 40(8), btae503

Contributing

Submit patches using GitHub pull requests or by sending a patch file to james.eapen@vai.org. We follow the tidyverse style guide using styler and lintr.

Owner

  • Name: James Eapen
  • Login: jamespeapen
  • Kind: user
  • Location: Van Andel Institute
  • Company: @huishenlab

PhD student in computational biology

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "ceas" in publications use:'
type: software
license: MIT
title: 'ceas: Cellular Energetics Analysis Software'
version: 1.2.1
doi: 10.1093/bioinformatics/btae503
abstract: Measuring cellular energetics is essential to understanding a matrix’s (e.g.
  cell, tissue or biofluid) metabolic state. The Agilent Seahorse machine is a common
  method to measure real-time cellular energetics, but existing analysis tools are
  highly manual or lack functionality. The Cellular Energetics Analysis Software (ceas)
  R package fills this analytical gap by providing modular and automated Seahorse
  data analysis and visualization using the methods described by Mookerjee et al.
  (2017) <https://doi.org/10.1074/jbc.m116.774471>.
authors:
- family-names: House
  given-names: Rachel (Rae) J.
  email: rachel.house@vai.org
  orcid: https://orcid.org/0000-0003-2176-0431
- family-names: Eapen
  given-names: James P.
  email: james.eapen@vai.org
  orcid: https://orcid.org/0000-0001-6016-3598
preferred-citation:
  type: article
  title: 'ceas: An R package for Seahorse data analysis and visualization'
  authors:
  - family-names: House
    given-names: Rachel (Rae) J.
    email: rachel.house@vai.org
    orcid: https://orcid.org/0000-0003-2176-0431
  - family-names: Eapen
    given-names: James P.
    email: james.eapen@vai.org
    orcid: https://orcid.org/0000-0001-6016-3598
  - family-names: Shen
    given-names: Hui
  - family-names: Graveel
    given-names: Carrie R.
  - family-names: Steensma
    given-names: Matthew R.
  journal: Bioinformatics
  year: '2024'
  volume: '40'
  issue: '8'
  doi: 10.1093/bioinformatics/btae503
  url: https://jamespeapen.github.io/ceas/
  start: btae503
repository: https://CRAN.R-project.org/package=ceas
repository-code: https://github.com/jamespeapen/ceas/issues/
url: https://jamespeapen.github.io/ceas/
contact:
- family-names: House
  given-names: Rachel (Rae) J.
  email: rachel.house@vai.org
  orcid: https://orcid.org/0000-0003-2176-0431
identifiers:
- type: url
  value: https://github.com/jamespeapen/ceas/

GitHub Events

Total
  • Create event: 5
  • Issues event: 2
  • Release event: 1
  • Delete event: 6
  • Push event: 23
Last Year
  • Create event: 5
  • Issues event: 2
  • Release event: 1
  • Delete event: 6
  • Push event: 23

Issues and Pull Requests

Last synced: 6 months ago

Packages

  • Total packages: 1
  • Total downloads:
    • cran 277 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: ceas

Cellular Energetics Analysis Software

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 277 Last month
Rankings
Dependent packages count: 27.8%
Dependent repos count: 35.6%
Average: 49.5%
Downloads: 85.1%
Maintainers (1)
rachel.house@vai.org
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • data.table * imports
  • readxl * imports
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite