Applications/PaCeQuantAna - Revision history

Moeller: /* Email */

2023-06-05T06:41:30Z

← Older revision		Revision as of 08:41, 5 June 2023
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	===== Email =====		===== Email =====
	[[file:Email.png\|left\|36px\|link=]]		[[file:Email.png\|left\|36px\|link=]]
	Don't hesitate to send an email when you encounter a problem or when you have questions: [mailto:poeschl@~~informatik~~.uni-halle.de poeschl@~~informatik~~.uni-halle.de]<br>		Don't hesitate to send an email when you encounter a problem or when you have questions: [mailto:yvonne.poeschl-grau@landw.uni-halle.de yvonne.poeschl-grau@landw.uni-halle.de]<br>

	<br>		<br>

Moeller: /* PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues */

2023-03-23T16:13:37Z

PaCeQuantAna: R package for Visualization and Statistical Analysis of Cell Shape Featues

← Older revision		Revision as of 18:13, 23 March 2023
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	The new version compatible with PaCeQuant as released in MiToBo 2.0 in May 2020 is out now! It can be downloaded here:		The new version compatible with PaCeQuant as released in MiToBo 2.0 in May 2020 is out now! It can be downloaded here:

	* [http://informatik.uni-halle.de/~~~poeschl~~/~~PaCeQuantAna~~/~~BookChapter2020~~/PaCeQuantAna_1.0.3.tar.gz R package v1.0.3]		* [http://www2.informatik.uni-halle.de/agprbio/mitobo/downloads/paceQuant/paceQuantAna/PaCeQuantAna_1.0.3.tar.gz R package v1.0.3]

Poeschl: /* Installation */

2020-11-27T08:38:54Z

Installation

← Older revision		Revision as of 10:38, 27 November 2020
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	</ul>		</ul>
	<ul> '''R versions >= 3.5.0''':		<ul> '''R versions >= 3.5.0''':
	<ul>If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:		<ul>If you do not have used Bioconductor before and have not installed any [http://bioconductor.org/install/ Bioconductor] packages yet, then:
	<blockquote>Install BiocManager and core packages from Bioconductor:		<blockquote>Install BiocManager and core packages from Bioconductor:
	<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))</blockquote>		<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))</blockquote>

Poeschl: /* Documentation */

2020-11-27T08:37:57Z

Documentation

← Older revision		Revision as of 10:37, 27 November 2020
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	You can directly copy the script into a file and load this file into the Rstudio editor to run it completely or line-wise.		You can directly copy the script into a file and load this file into the Rstudio editor to run it completely or line-wise.

	You can test the new version of the package with sample data and small workflows for analyses of developmental stages and mutant screening. Therefore we provide two archives:		You can test the new version of the package with sample data and small workflows (R scripts) for analyses of developmental stages and mutant screening. Therefore we provide two archives:

	* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/developmentalStages.zip Sample data and ~~workflow~~ for analyses of developmental stages]		* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/developmentalStages.zip Sample data and R scripts for analyses of developmental stages]

	* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/mutantScreening.zip Sample data and ~~workflow~~ for mutant screening]		* [http://informatik.uni-halle.de/~poeschl/PaCeQuantAna/BookChapter2020/mutantScreening.zip Sample data and R scripts for mutant screening]

	Both archives contain the specific <br>		Both archives contain the specific <br>
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	</ul>		</ul>
	</ul>		</ul>


	=== Important notes ===		=== Important notes ===

Poeschl: /* Installation */

2020-11-27T08:35:55Z

Installation

Poeschl: /* Installation */

2020-11-27T08:34:37Z

Installation

← Older revision		Revision as of 10:34, 27 November 2020
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	<ul> '''R versions >= 3.5.0''':		<ul> '''R versions >= 3.5.0''':
	<blockquote>If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:		<blockquote>If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:
	<ul> Install BiocManager and core packages from Bioconductor:		<blockquote>Install BiocManager and core packages from Bioconductor:
	<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))		<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))
	<blockquote>install.packages("BiocManager")		<blockquote>install.packages("BiocManager")
	<blockquote>BiocManager::install()		<blockquote>BiocManager::install()
	~~</ul>~~
	<ul>Install specific packages e.g. "multtest"		<blockquote>Install specific packages e.g. "multtest"
	<blockquote>BiocManager::install("multtest")		<blockquote>BiocManager::install("multtest")
	~~</ul>~~
	</ul>		</ul>
	<li> Install the PaCeQuantAna package selecting		<li> Install the PaCeQuantAna package selecting

Poeschl: /* Installation */

2020-11-27T08:33:25Z

Installation

← Older revision		Revision as of 10:33, 27 November 2020
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	</ul>		</ul>
	<ul> '''R versions >= 3.5.0''':		<ul> '''R versions >= 3.5.0''':
	<blockquote> If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:		<blockquote>If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:
	<ul> Install BiocManager and core packages from Bioconductor:		<ul> Install BiocManager and core packages from Bioconductor:
	<blockquote> if (!requireNamespace("BiocManager", quietly = TRUE))		<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))
	<blockquote> install.packages("BiocManager")		<blockquote>install.packages("BiocManager")
	<blockquote> BiocManager::install()		<blockquote>BiocManager::install()
	</ul>		</ul>
	<ul> Install specific packages e.g. "multtest"		<ul>Install specific packages e.g. "multtest"
	<blockquote> BiocManager::install("multtest")		<blockquote>BiocManager::install("multtest")
	</ul>		</ul>
	</ul>		</ul>

Poeschl: /* Installation */

2020-11-27T08:32:52Z

Installation

← Older revision		Revision as of 10:32, 27 November 2020
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	<ul> '''R versions >= 3.5.0''':		<ul> '''R versions >= 3.5.0''':
	<blockquote> If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:		<blockquote> If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:
	<ul> Install BiocManager and core packages from Bioconductor		<ul> Install BiocManager and core packages from Bioconductor:
	<blockquote> if (!requireNamespace("BiocManager", quietly = TRUE))		<blockquote> if (!requireNamespace("BiocManager", quietly = TRUE))
	install.packages("BiocManager")		<blockquote> install.packages("BiocManager")
	BiocManager::install()		<blockquote> BiocManager::install()
			</ul>
			<ul> Install specific packages e.g. "multtest"
			<blockquote> BiocManager::install("multtest")
	</ul>		</ul>
	~~<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote>~~
	~~<blockquote>biocLite("multtest")</blockquote>~~
	</ul>		</ul>
	<li> Install the PaCeQuantAna package selecting		<li> Install the PaCeQuantAna package selecting

Poeschl: /* Installation */

2020-11-27T08:30:01Z

Installation

← Older revision		Revision as of 10:30, 27 November 2020
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	from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote>		from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote>
	<li> The multtest package can be installed via the following Bioconductor installation script:<br>		<li> The multtest package can be installed via the following Bioconductor installation script:<br>
	<ul> R versions < 3.5.0:		<ul> '''R versions < 3.5.0''':
			<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote>
			<blockquote>biocLite("multtest")</blockquote>
			</ul>
			<ul> '''R versions >= 3.5.0''':
			<blockquote> If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:
			<ul> Install BiocManager and core packages from Bioconductor
			<blockquote> if (!requireNamespace("BiocManager", quietly = TRUE))
			install.packages("BiocManager")
			BiocManager::install()
			</ul>
	<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote>		<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote>
	<blockquote>biocLite("multtest")</blockquote>		<blockquote>biocLite("multtest")</blockquote>

Poeschl: /* Installation */

2020-11-27T08:25:04Z

Installation

← Older revision		Revision as of 10:25, 27 November 2020
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	from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote>		from the menu bar.<br> Choose <blockquote>“Install from: Repository (CRAN)”</blockquote> and enter the names of the packages.<br> Activate <blockquote>“Install dependencies”.</blockquote>
	<li> The multtest package can be installed via the following Bioconductor installation script:<br>		<li> The multtest package can be installed via the following Bioconductor installation script:<br>
			<ul> R versions < 3.5.0:
	<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote>		<blockquote>source ("<nowiki>http://bioconductor.org/biocLite.R</nowiki>")</blockquote>
	<blockquote>biocLite("multtest")</blockquote>		<blockquote>biocLite("multtest")</blockquote>
			</ul>
	<li> Install the PaCeQuantAna package selecting		<li> Install the PaCeQuantAna package selecting
	<blockquote>“Tools” → “Install Packages…”</blockquote>		<blockquote>“Tools” → “Install Packages…”</blockquote>

← Older revision		Revision as of 10:35, 27 November 2020
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	</ul>		</ul>
	<ul> '''R versions >= 3.5.0''':		<ul> '''R versions >= 3.5.0''':
	<~~blockquote~~>If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:		<ul>If you do not have used Bioconductor before and have not installed any Bioconductor packages yet, then:
	<blockquote>Install BiocManager and core packages from Bioconductor:		<blockquote>Install BiocManager and core packages from Bioconductor:
	<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))		<blockquote>if (!requireNamespace("BiocManager", quietly = TRUE))</blockquote>
	<blockquote>install.packages("BiocManager")		<blockquote>install.packages("BiocManager")</blockquote>
	<blockquote>BiocManager::install()		<blockquote>BiocManager::install()</blockquote>
			</ul>
	<~~blockquote~~>Install specific packages e.g. "multtest"		<ul>Install specific packages e.g. "multtest"
	<blockquote>BiocManager::install("multtest")		<blockquote>BiocManager::install("multtest")</blockquote>
			</ul>
	</ul>		</ul>
	<li> Install the PaCeQuantAna package selecting		<li> Install the PaCeQuantAna package selecting