Package: topologyGSA 1.5.0
Gabriele Sales
topologyGSA: Gene Set Analysis Exploiting Pathway Topology
Using Gaussian graphical models we propose a novel approach to perform pathway analysis using gene expression. Given the structure of a graph (a pathway) we introduce two statistical tests to compare the mean and the concentration matrices between two groups. Specifically, these tests can be performed on the graph and on its connected components (cliques). The package is based on the method described in Massa M.S., Chiogna M., Romualdi C. (2010) <doi:10.1186/1752-0509-4-121>.
Authors:
topologyGSA_1.5.0.tar.gz
topologyGSA_1.5.0.tar.gz(r-4.5-noble)topologyGSA_1.5.0.tar.gz(r-4.4-noble)
topologyGSA_1.5.0.tgz(r-4.4-emscripten)topologyGSA_1.5.0.tgz(r-4.3-emscripten)
topologyGSA.pdf |topologyGSA.html✨
topologyGSA/json (API)
| # Install 'topologyGSA' in R: |
| install.packages('topologyGSA', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 12 months agofrom:68c5de1776. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 20 2024 |
| R-4.5-linux | OK | Aug 20 2024 |
Exports:clique.mean.testclique.var.testpathway.mean.testpathway.var.testrender.significant.cliques
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArraydotCall64fastmapfieldsformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphgRbasehttrigraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrmapsMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormopensslpkgconfigplogrpngqpgraphqtlR6RcppRcppArmadilloRcppEigenRCurlrestfulrRgraphvizRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowspamSparseArraySummarizedExperimentsysUCSC.utilsvctrsviridisLiteXMLxtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Comparison of all the cliques of a pathway. | clique.mean.test |
| Testing the concentration matrices of all cliques of a pathway. | clique.var.test |
| DAG representation of the B cell receptor signaling pathway | dag_bcell |
| Testing the means of a pathway. | pathway.mean.test |
| Testing the concentration matrices of a pathway. | pathway.var.test |
| Print results of statistical tests. | print.clique.mean.test print.clique.var.test print.pathway.mean.test print.pathway.var.test |
| Graphical display of the significant cliques | render.significant.cliques |
| Gene expression signatures in acute lymphocytic leukemia for BCR signaling pathway | y1 |
| Gene expression signatures in acute lymphocytic leukemia for BCR signaling pathway | y2 |