Package: transcriptogramer 1.29.0

Diego Morais

transcriptogramer: Transcriptional analysis based on transcriptograms

R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.

Authors:Diego Morais [aut, cre], Rodrigo Dalmolin [aut]

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transcriptogramer.pdf |transcriptogramer.html✨
transcriptogramer/json (API)
NEWS

# Install 'transcriptogramer' in R:
install.packages('transcriptogramer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/arthurvinx/transcriptogramer/issues

Datasets:
  • DEsymbols - Dictionary Protein2Symbol
  • 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
  • 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
  • association - Association

On BioConductor:transcriptogramer-1.29.0(bioc 3.21)transcriptogramer-1.28.0(bioc 3.20)

softwarenetworkvisualizationsystemsbiologygeneexpressiongenesetenrichmentgraphandnetworkclusteringdifferentialexpressionmicroarrayrnaseqtranscriptionimmunooncology

4.81 score 4 stars 8 scripts 228 downloads 2 mentions 13 exports 92 dependencies

Last updated 23 days agofrom:c3aae60638. Checks:OK: 4 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macOKOct 31 2024

Exports:clusterEnrichmentclusterVisualizationconnectivityPropertiesDEdifferentiallyExpressedenrichmentPlotorderingPropertiesradiusradius<-TermstranscriptogramPreprocesstranscriptogramStep1transcriptogramStep2

Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrdigestdoSNOWdplyrfansifarverfastmapfilelockforeachgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgraphgtablehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclelimmamagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRedeRrlangRSQLiteS4VectorsscalessnowSparseMstatmodstringistringrsystibbletidyrtidyselecttopGOUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc

The transcriptogramer user's guide

Diego Morais, Rodrigo Dalmolin

Rendered fromtranscriptogramer.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-11-19
Started: 2017-10-02

Readme and manuals

Help Manual

Help pageTopics
Transcriptional analysis based on transcriptogramstranscriptogramer-package transcriptogramer
Associationassociation
Term enrichmentclusterEnrichment clusterEnrichment,Transcriptogram-method clusterEnrichment-method
Displays graphs of the differentially expressed clustersclusterVisualization clusterVisualization,Transcriptogram-method clusterVisualization-method
Calculates average graph properties as function of node connectivityconnectivityProperties connectivityProperties,Transcriptogram-method connectivityProperties-method
Get DEDE DE,Transcriptogram-method DE-method
Dictionary Protein2SymbolDEsymbols
Identify which genes are differentially expresseddifferentiallyExpressed differentiallyExpressed,Transcriptogram-method differentiallyExpressed-method
Projects Gene Ontology terms on the orderingenrichmentPlot enrichmentPlot,Transcriptogram-method enrichmentPlot-method
Dictionary Protein2ProbeGPL570
Dataset containing expression valuesGSE9988
Ordered Homo sapiens proteins of combined score greater than or equal to 700Hs700
Ordered Homo sapiens proteins of combined score greater than or equal to 800Hs800
Ordered Homo sapiens proteins of combined score greater than or equal to 900Hs900
Dictionary Protein2GOHsBPTerms
Ordered Mus musculus proteins of combined score greater than or equal to 700Mm700
Ordered Mus musculus proteins of combined score greater than or equal to 800Mm800
Ordered Mus musculus proteins of combined score greater than or equal to 900Mm900
Calculates graph properties projected on the ordered proteinsorderingProperties orderingProperties,Transcriptogram-method orderingProperties-method
Radiusradius radius,Transcriptogram-method radius-method radius<- radius<-,Transcriptogram-method
Ordered Rattus norvegicus proteins of combined score greater than or equal to 700Rn700
Ordered Rattus norvegicus proteins of combined score greater than or equal to 800Rn800
Ordered Rattus norvegicus proteins of combined score greater than or equal to 900Rn900
Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 700Sc700
Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 800Sc800
Ordered Saccharomyces cerevisiae proteins of combined score greater than or equal to 900Sc900
Get termsTerms Terms,Transcriptogram-method Terms-method
Class TranscriptogramTranscriptogram-class
Creates an object of class TranscriptogramtranscriptogramPreprocess
Calculates the average of the expression values related to the same proteintranscriptogramStep1 transcriptogramStep1,Transcriptogram-method transcriptogramStep1-method
Calculates the average of the expression values using a sliding windowtranscriptogramStep2 transcriptogramStep2,Transcriptogram-method transcriptogramStep2-method