Cytobank API Wrapper for R

Tools to interface with Cytobank's API via R, organized by various endpoints that represent various areas of Cytobank functionality. Learn more about Cytobank at < https://www.cytobank.org>.


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Overview

The CytobankAPI package is designed to make interacting with Cytobank API endpoints easy via R. View the Cytobank API Endpoint Documentation for a comprehensive list of API endpoints for Cytobank.

To find more general documentation on using the CytobankAPI package, view the Cytobank quickstart guide.

Installation

install.packages("CytobankAPI")

News

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CytobankAPI 1.1.0

  • DROP endpoints added:

    • drop.upload & drop.upload_zip allow users to upload DROP files (CSV, TSV, TXT, FCS) to Cytobank
  • Statistics endpoint changes:

    • Allow long channel names to be used instead of channel IDs via the statistics.general endpoint
    • Get experiment version for user
    • Fixed bug involving experiments with no gates (was not able to gather statistics because no populations present in API response)
      • Now experiments with no gates are correctly gathering statistics
  • Advanced Analyses:

    • Allow long channel names to be used for advanced analyses objects

CytobankAPI 1.0.1.1

  • Bug fixes:

    • spade.bubbles_set endpoint correctly sending API requests using named named bubble list of node vectors
  • SPADE endpoint changes:

    • Allow 'absolute number' settings for Downsampled Events Target
    • Exposing 'created experiment' for SPADE analyses
  • Helper functions:

    • Added helper.channel_ids_from_long_names
      • Allow short channel names to be used instead of IDs
  • Implementing startup message to view CytobankAPI NEWS (via the 'CytobankAPI_news()' function)


CytobankAPI 1.0.1

  • Added a NEWS.md file to track changes to the package.

  • SPADE endpoint changes:

    • Added downloading GML support
    • Added downloading full SPADE analysis support
    • Support updating the SPADE name directly via the spade.update method
  • viSNE endpoint changes:

    • Added viSNE 2.0 settings
  • Updated general documentation

Reference manual

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install.packages("CytobankAPI")

1.1.2 by Preston Ng, 14 days ago


Browse source code at https://github.com/cran/CytobankAPI


Authors: Preston Ng [aut, cre], Chris Ciccolella [aut], Katherine Drake [aut]


Documentation:   PDF Manual  


Artistic-2.0 license


Imports jsonlite, methods, stats

Depends on curl, httr

Suggests knitr, rmarkdown, testthat


Imported by CytobankAPIstats.

Depended on by CytobankBridgeR.


See at CRAN