topologyGSA
Gene Set Analysis Exploiting Pathway Topology
Description
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>.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | ERROR |
| r-release-windows-x86_64 | OK |
Check details (3 non-OK)
CRAN incoming feasibility
Maintainer: ‘Gabriele Sales <gabriele.sales@unipd.it>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Sofia",
family = "Massa",
role = "aut"),
person(given = "Gabriele",
family = "Sales",
role = c("aut", "cre"),
email = "gabriele.sales@unipd.it"))
as necessary.
CRAN incoming feasibility
Maintainer: ‘Gabriele Sales <gabriele.sales@unipd.it>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Sofia",
family = "Massa",
role = "aut"),
person(given = "Gabriele",
family = "Sales",
role = c("aut", "cre"),
email = "gabriele.sales@unipd.it"))
as necessary.
package dependencies
Package required but not available: ‘qpgraph’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
Check History
ERROR 11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
CRAN incoming feasibility
Maintainer: ‘Gabriele Sales <gabriele.sales@unipd.it>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Sofia",
family = "Massa",
role = "aut"),
person(given = "Gabriele",
family = "Sales",
role = c("aut", "cre"),
email = "gabriele.sales@unipd.it"))
as necessary.
CRAN incoming feasibility
Maintainer: ‘Gabriele Sales <gabriele.sales@unipd.it>’
No Authors@R field in DESCRIPTION.
Please add one, modifying
Authors@R: c(person(given = "Sofia",
family = "Massa",
role = "aut"),
person(given = "Gabriele",
family = "Sales",
role = c("aut", "cre"),
email = "gabriele.sales@unipd.it"))
as necessary.
package dependencies
Package required but not available: ‘qpgraph’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.