Package: CoSIA 1.5.4

Amanda D. Clark

CoSIA: An Investigation Across Different Species and Tissues

Cross-Species Investigation and Analysis (CoSIA) is a package that provides researchers with an alternative methodology for comparing across species and tissues using normal wild-type RNA-Seq Gene Expression data from Bgee. Using RNA-Seq Gene Expression data, CoSIA provides multiple visualization tools to explore the transcriptome diversity and variation across genes, tissues, and species. CoSIA uses the Coefficient of Variation and Shannon Entropy and Specificity to calculate transcriptome diversity and variation. CoSIA also provides additional conversion tools and utilities to provide a streamlined methodology for cross-species comparison.

Authors:Anisha Haldar [aut], Vishal H. Oza [aut], Amanda D. Clark [cre, aut], Nathaniel S. DeVoss [aut], Brittany N. Lasseigne [aut]

CoSIA_1.5.4.tar.gz
CoSIA_1.5.4.zip(r-4.5)CoSIA_1.5.4.zip(r-4.4)CoSIA_1.5.4.zip(r-4.3)

CoSIA_1.5.4.tar.gz(r-4.5-noble)CoSIA_1.5.4.tar.gz(r-4.4-noble)
CoSIA_1.5.4.tgz(r-4.4-emscripten)CoSIA_1.5.4.tgz(r-4.3-emscripten)
CoSIA.pdf |CoSIA.html
CoSIA/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/lasseignelab/cosia/issues

On BioConductor:CoSIA-1.5.4(bioc 3.20)CoSIA-1.4.2(bioc 3.19)

softwarebiologicalquestiongeneexpressionmultiplecomparisonthirdpartyclientdataimportgui

5.60 score 5 stars 3 scripts 64 downloads 10 exports 118 dependencies

Last updated 6 days agofrom:c945c082ca. Checks:OK: 2 ERROR: 1 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-winNOTEOct 26 2024
R-4.5-linuxERROROct 28 2024
R-4.4-winNOTEOct 26 2024
R-4.3-winOKOct 26 2024

Exports:CoSIAngetConversiongetGExgetGExMetricsgetTissuesplotCVGExplotDSGExplotSpeciesGExplotTissueGExviewCoSIAn

Dependencies:AnnotationDbiAnnotationHubannotationToolsaskpassbase64encBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionbiomaRtBiostringsbitbit64blobbslibcachemclicliprcolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrdigestdplyrevaluateExperimentHubfansifarverfastmapfilelockfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegtablehighrhmshomologenehtmltoolshtmlwidgetshttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslorg.Ce.eg.dborg.Dm.eg.dborg.Dr.eg.dborg.Hs.eg.dborg.Mm.eg.dborg.Rn.eg.dbpillarpkgconfigplogrplotlypngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrlangrmarkdownRSQLiteS4VectorssassscalesstringistringrsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunxml2XVectoryamlzlibbioc

CoSIA, an R package for Cross Species Investigation and Analysis

Rendered fromCoSIA_Intro.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-10-18
Started: 2022-12-08

Readme and manuals

Help Manual

Help pageTopics
CoSIAn Class S4 ObjectCoSIAn-class
Constructor for the CoSIAn ObjectCoSIAn CoSIAn-Constructor Constructor for the CoSIAn Class
getConversion GenericgetConversion
getConversion MethodgetConversion,CoSIAn-method
getGEx GenericgetGEx
getGEx MethodgetGEx,CoSIAn-method
getGExMetrics GenericgetGExMetrics
getGExMetrics MethodgetGExMetrics,CoSIAn-method
getTissuesgetTissues
plotCVGEx GenericplotCVGEx
plotCVGEx MethodplotCVGEx,CoSIAn-method
plotDSGEx GenericplotDSGEx
plotDSGEx MethodplotDSGEx,CoSIAn-method
plotSpeciesGEx GenericplotSpeciesGEx
plotSpeciesGEx MethodplotSpeciesGEx,CoSIAn-method
plotTissueGEx GenericplotTissueGEx
plotTissueGEx MethodplotTissueGEx,CoSIAn-method
viewCoSIAn GenericsviewCoSIAn
viewCoSIAnviewCoSIAn,CoSIAn-method