Package: SpeCond 1.67.0

Florence Cavalli

SpeCond: Condition specific detection from expression data

This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.

Authors:Florence Cavalli

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SpeCond/json (API)

# Install 'SpeCond' in R:

install.packages('SpeCond', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

expressionSpeCondExample - The expression matrix example used in the SpeCond package
expSetSpeCondExample - An ExpressionSet example object used in the SpeCond package
simulatedSpeCondData - An example of simulated expression matrix used in the SpeCond package

On BioConductor:SpeCond-1.67.0(bioc 3.24)SpeCond-1.66.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

microarray differentialexpression multiplecomparison clustering reportwriting

3.92 score 14 scripts 3 mentions 14 exports 12 dependencies

Last updated from:4208a6d4e7. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	138
linux-devel-x86_64	NOTE	203
source / vignettes	OK	195
linux-release-x86_64	NOTE	169
macos-release-arm64	NOTE	88
macos-oldrel-arm64	NOTE	90
windows-devel	NOTE	114
windows-release	NOTE	166
windows-oldrel	NOTE	122
wasm-release	OK	142

Exports:createParameterMatrix fitNoPriorWithExclusion fitPrior getDefaultParameter getFullHtmlSpeCondResult getGeneHtmlPage getMatrixFromExpressionSet getProfile getSpecificOutliersStep1 getSpecificResult SpeCond writeGeneResult writeSpeCondResult writeUniqueProfileSpecificResult

Dependencies:Biobase BiocGenerics dotCall64 fields generics hwriter maps mclust RColorBrewer Rcpp spam viridisLite

SpeCond

Rendered fromSpeCond.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Help page	Topics
Create or Modify the SpeCond argument parameters	createParameterMatrix
The expression matrix example used in the SpeCond package	expressionSpeCondExample
An ExpressionSet example object used in the SpeCond package	expSetSpeCondExample
Fit the expression values profile with a mixture of normal components ignoring outliers	fitNoPriorWithExclusion
Fit the expression value profiles with a mixture of normal components	fitPrior
Get the default parameter to use SpeCond function	getDefaultParameter
Visualisation function of the SpeCond analysis results	getFullHtmlSpeCondResult
Visualise for each gene the condition-specific detection result from SpeCond	getGeneHtmlPage
Obtain the expression matrix from an ExpressionSet object	getMatrixFromExpressionSet
Create the condition-specific profile of specific matrix result from SpeCond	getProfile
Detect the condition-specific as outliers in for the first step on the SpeCond procedure	getSpecificOutliersStep1
Detect the condition-specific genes for the second step on the SpeCond procedure	getSpecificResult
An example of simulated expression matrix used in the SpeCond package	simulatedSpeCondData
The condition-specific detection function	SpeCond
Write a condition-specific analysis result text file	writeGeneResult
Write in text files the main result of the SpeCond function	writeSpeCondResult
Write the specific profiles from the SpeCond analysis	writeUniqueProfileSpecificResult

Package: SpeCond 1.67.0

SpeCond: Condition specific detection from expression data

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Usage by other packages (reverse dependencies)