easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.

High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput mi...

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Autores principales:	Joy Nyaanga, Timothy A Crombie, Samuel J Widmayer, Erik C Andersen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/c5c23f79ad0742589fc7d78eb2d7aa61
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spelling	oai:doaj.org-article:c5c23f79ad0742589fc7d78eb2d7aa612021-12-02T20:18:19ZeasyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.1932-620310.1371/journal.pone.0252000https://doaj.org/article/c5c23f79ad0742589fc7d78eb2d7aa612021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0252000https://doaj.org/toc/1932-6203High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler's WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.Joy NyaangaTimothy A CrombieSamuel J WidmayerErik C AndersenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 8, p e0252000 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Joy Nyaanga Timothy A Crombie Samuel J Widmayer Erik C Andersen easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
description	High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler's WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.
format	article
author	Joy Nyaanga Timothy A Crombie Samuel J Widmayer Erik C Andersen
author_facet	Joy Nyaanga Timothy A Crombie Samuel J Widmayer Erik C Andersen
author_sort	Joy Nyaanga
title	easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
title_short	easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
title_full	easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
title_fullStr	easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
title_full_unstemmed	easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.
title_sort	easyxpress: an r package to analyze and visualize high-throughput c. elegans microscopy data generated using cellprofiler.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/c5c23f79ad0742589fc7d78eb2d7aa61
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easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler.

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