Package: SANTA 2.43.0
Alex Cornish
SANTA: Spatial Analysis of Network Associations
This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode).
Authors:
SANTA_2.43.0.tar.gz
SANTA_2.43.0.zip(r-4.5)SANTA_2.43.0.zip(r-4.4)SANTA_2.43.0.zip(r-4.3)
SANTA_2.43.0.tgz(r-4.4-x86_64)SANTA_2.43.0.tgz(r-4.4-arm64)SANTA_2.43.0.tgz(r-4.3-x86_64)SANTA_2.43.0.tgz(r-4.3-arm64)
SANTA_2.43.0.tar.gz(r-4.5-noble)SANTA_2.43.0.tar.gz(r-4.4-noble)
SANTA_2.43.0.tgz(r-4.4-emscripten)SANTA_2.43.0.tgz(r-4.3-emscripten)
SANTA.pdf |SANTA.html✨
SANTA/json (API)
NEWS
| # Install 'SANTA' in R: |
| install.packages('SANTA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/alexjcornish/santa/issues
- edgelist.humannet - Pre-processed dataset for the SANTA vignette
- edgelist.intact - Pre-processed dataset for the SANTA vignette
- g.bandyopadhyay.treated - Pre-processed dataset for the SANTA vignette
- g.bandyopadhyay.untreated - Pre-processed dataset for the SANTA vignette
- g.costanzo.cor - Pre-processed dataset for the SANTA vignette
- g.costanzo.raw - Pre-processed dataset for the SANTA vignette
- g.srivas.high - Pre-processed dataset for the SANTA vignette
- g.srivas.untreated - Pre-processed dataset for the SANTA vignette
- go.entrez - Pre-processed dataset for the SANTA vignette
- rnai.cheung - Pre-processed dataset for the SANTA vignette
On BioConductor:SANTA-2.43.0(bioc 3.21)SANTA-2.42.0(bioc 3.20)
networknetworkenrichmentclustering
Last updated 2 months agofrom:95b5b44627. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win-x86_64 | OK | Dec 18 2024 |
| R-4.5-linux-x86_64 | OK | Dec 18 2024 |
| R-4.4-win-x86_64 | OK | Dec 18 2024 |
| R-4.4-mac-x86_64 | OK | Dec 18 2024 |
| R-4.4-mac-aarch64 | OK | Dec 18 2024 |
| R-4.3-win-x86_64 | OK | Dec 18 2024 |
| R-4.3-mac-x86_64 | OK | Dec 18 2024 |
| R-4.3-mac-aarch64 | OK | Dec 18 2024 |
Exports:BinGraphCompactnessCreateGridDistGraphGraphDiffusionGraphMFPTKnetKnodeplot.KnetSpreadHits
Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigrlangvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute a distance bin matrix from a distance matrix | BinGraph |
| Measure the strength of association using compactness scores | Compactness |
| Generate a grid-like network | CreateGrid |
| Compute the vertex pair distance matrix for a graph | DistGraph |
| Compute diffusion kernel-based distance matrix | GraphDiffusion |
| Compute mean first-passage time-based distance matrix | GraphMFPT |
| Measure the strength of association between a phenotype and a network by computing the strength of hit clustering on the network | Knet |
| Rank vertices by their strength of association with high-weight vertices | Knode |
| Plot the results of the 'Knet' function | plot.Knet |
| Pre-processed dataset for the SANTA vignette | edgelist.humannet edgelist.intact g.bandyopadhyay.treated g.bandyopadhyay.untreated g.costanzo.cor g.costanzo.raw g.srivas.high g.srivas.untreated go.entrez rnai.cheung |
| Spread hits across a network in clusters | SpreadHits |