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:Sofia Massa, Gabriele Sales

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'))

Peer review:

Datasets:
  • dag_bcell - DAG representation of the B cell receptor signaling pathway
  • y1 - Gene expression signatures in acute lymphocytic leukemia for BCR signaling pathway
  • y2 - Gene expression signatures in acute lymphocytic leukemia for BCR signaling pathway

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.60 score 9 scripts 301 downloads 4 mentions 5 exports 87 dependencies

Last updated 1 years agofrom:68c5de1776. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linuxOKDec 01 2024

Exports:clique.mean.testclique.var.testpathway.mean.testpathway.var.testrender.significant.cliques

Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemclicodetoolscpp11crayoncurlDBIDelayedArraydotCall64fastmapfieldsformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluegraphgRbasehttrigraphIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrmapsMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormopensslpkgconfigplogrpngqpgraphqtlR6RcppRcppArmadilloRcppEigenRCurlrestfulrRgraphvizRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowspamSparseArraySummarizedExperimentsysUCSC.utilsvctrsviridisLiteXMLxtableXVectoryamlzlibbioc