Package: SpeCond 1.59.0

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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SpeCond.pdf |SpeCond.html✨
SpeCond/json (API)

# Install 'SpeCond' in R:

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

Datasets:

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

On BioConductor:SpeCond-1.59.0(bioc 3.20)SpeCond-1.58.0(bioc 3.19)

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

bioconductor-package

14 exports 1.51 score 11 dependencies 3 mentions

Last updated 2 months agofrom:0224a84e5c

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

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

SpeCond

Rendered fromSpeCond.Rnwusingutils::Sweaveon Jul 03 2024.

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 1.59.0

SpeCond: Condition specific detection from expression data

SpeCond

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