pathVar: Methods to Find Pathways with Significantly Different Variability

This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.

AuthorLaurence de Torrente, Samuel Zimmerman, Jessica Mar
Date of publicationNone
MaintainerSamuel Zimmerman <sezimmer@einstein.yu.edu>
LicenseLGPL (>= 2.0)
Version1.4.0

View on Bioconductor

Man pages

bock: Gene Expression Matrix of Published Data

diagnosticsVarPlots: Plots the average expression against variability using...

diagnosticsVarPlotsTwoSample: Plots the average expression against variability using...

geneDistributionSet2-class: Class '"pathVarTwoSamplesCont"'

geneDistributionSet3-class: Class '"pathVarTwoSamplesDisc"'

geneDistributionSet-class: Class '"geneDistributionSet"'

geneSet-class: Class '"geneSet"'

getGenes: Gets significant genes within a certain window of...

makeDBList: Puts your own list of pathways and genes related to them into...

pathVarOneSample: Compares the distribution of genes in each cluster to the...

pathVar-package: Detects pathways with different levels of variance than...

pathVarTwoSamplesCont: Compares the distribution of genes in each pathway for two...

pathVarTwoSamplesDisc: Compares the number of genes in clusters in each pathway for...

plotAllTwoSampleDistributionCounts: Compares the distribution of genes in clusters for every gene...

plotPway: Checks if an object is from the one sample or two samples...

pways.kegg: List containing pathway IDs, names, and genes in each pathway

pways.reactome: List containing pathway IDs, names, and genes in each pathway

saveAsPDF: Save the plots of the significant pathway or a chosen list of...

significantPathway2-class: Class '"significantPathway2"'

significantPathway3-class: Class '"significantPathway3"'

significantPathway-class: Class '"significantPathway"'

sigPway: A function checks if an object is from the one sample or two...

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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