Transcriptional analysis based on transcriptograms

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Documentation for package ‘transcriptogramer’ version 1.26.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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transcriptogramer-package	Transcriptional analysis based on transcriptograms
association	Association
clusterEnrichment	Term enrichment
clusterEnrichment-method	Term enrichment
clusterVisualization	Displays graphs of the differentially expressed clusters
clusterVisualization-method	Displays graphs of the differentially expressed clusters
connectivityProperties	Calculates average graph properties as function of node connectivity
connectivityProperties-method	Calculates average graph properties as function of node connectivity
DE	Get DE
DE-method	Get DE
DEsymbols	Dictionary Protein2Symbol
differentiallyExpressed	Identify which genes are differentially expressed
differentiallyExpressed-method	Identify which genes are differentially expressed
enrichmentPlot	Projects Gene Ontology terms on the ordering
enrichmentPlot-method	Projects Gene Ontology terms on the ordering
GPL570	Dictionary Protein2Probe
GSE9988	Dataset containing expression values
Hs700	Ordered Homo sapiens proteins of combined score greater than or equal to 700
Hs800	Ordered Homo sapiens proteins of combined score greater than or equal to 800
Hs900	Ordered Homo sapiens proteins of combined score greater than or equal to 900
HsBPTerms	Dictionary Protein2GO
Mm700	Ordered Mus musculus proteins of combined score greater than or equal to 700
Mm800	Ordered Mus musculus proteins of combined score greater than or equal to 800
Mm900	Ordered Mus musculus proteins of combined score greater than or equal to 900
orderingProperties	Calculates graph properties projected on the ordered proteins
orderingProperties-method	Calculates graph properties projected on the ordered proteins
radius	Radius
radius-method	Radius
radius<-	Radius
radius<--method	Radius
Rn700	Ordered Rattus norvegicus proteins of combined score greater than or equal to 700
Rn800	Ordered Rattus norvegicus proteins of combined score greater than or equal to 800
Rn900	Ordered Rattus norvegicus proteins of combined score greater than or equal to 900
Sc700	Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700
Sc800	Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800
Sc900	Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900
Terms	Get terms
Terms-method	Get terms
Transcriptogram-class	Class Transcriptogram
transcriptogramer	Transcriptional analysis based on transcriptograms
transcriptogramPreprocess	Creates an object of class Transcriptogram
transcriptogramStep1	Calculates the average of the expression values related to the same protein
transcriptogramStep1-method	Calculates the average of the expression values related to the same protein
transcriptogramStep2	Calculates the average of the expression values using a sliding window
transcriptogramStep2-method	Calculates the average of the expression values using a sliding window