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 |