# Transcriptional analysis based on transcriptograms

## Documentation for package ‘transcriptogramer’ version 1.14.0

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

## Help Pages

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