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:
transcriptogramer_1.29.0.tar.gz
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transcriptogramer_1.29.0.tgz(r-4.4-any)transcriptogramer_1.29.0.tgz(r-4.3-any)
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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')) |
Bug tracker:https://github.com/arthurvinx/transcriptogramer/issues
- 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
Last updated 2 months agofrom:c3aae60638. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 30 2024 |
| R-4.5-win | OK | Nov 30 2024 |
| R-4.5-linux | OK | Nov 30 2024 |
| R-4.4-win | OK | Nov 30 2024 |
| R-4.4-mac | OK | Nov 30 2024 |
| R-4.3-win | OK | Nov 30 2024 |
| R-4.3-mac | OK | Nov 30 2024 |
Exports:clusterEnrichmentclusterVisualizationconnectivityPropertiesDEdifferentiallyExpressedenrichmentPlotorderingPropertiesradiusradius<-TermstranscriptogramPreprocesstranscriptogramStep1transcriptogramStep2
Dependencies:AnnotationDbiaskpassBiobaseBiocFileCacheBiocGenericsbiomaRtBiostringsbitbit64blobcachemclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrdigestdoSNOWdplyrfansifarverfastmapfilelockforeachgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgraphgtablehmshttrhttr2igraphIRangesisobanditeratorsjsonliteKEGGRESTlabelinglatticelifecyclelimmamagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRedeRrlangRSQLiteS4VectorsscalessnowSparseMstatmodstringistringrsystibbletidyrtidyselecttopGOUCSC.utilsutf8vctrsviridisLitewithrxml2XVectorzlibbioc
