Package: divergence 0.99.07
Wikum Dinalankara
divergence: Divergence: Functionality for assessing omics data by divergence with respect to a baseline
This package provides functionality for performing divergence analysis as presented in Dinalankara et al, "Digitizing omics profiles by divergence from a baseline", PANS 2018. This allows the user to simplify high dimensional omics data into a binary or ternary format which encapsulates how the data is divergent from a specified baseline group with the same univariate or multivariate features.
Authors:
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divergence.pdf |divergence.html✨
divergence/json (API)
| # Install 'divergence' in R: |
| install.packages('divergence', repos = c('https://marchionnilab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/marchionnilab/divergence/issues
- breastTCGA_ER - ER positive or negative status of breast tumor samples
- breastTCGA_Group - Normal or Tumor status of breast samples
- breastTCGA_Mat - Gene expression for 260 genes in 887 breast samples
- msigdb_Hallmarks - Cancer Hallmark gene sets from the MSigDB collection
On BioConductor:divergence-1.23.0(bioc 3.21)divergence-1.22.0(bioc 3.20)
Last updated 4 years agofrom:dabfeb303e. Checks:1 OK, 8 NOTE. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 13 2025 |
| R-4.5-win | NOTE | Mar 13 2025 |
| R-4.5-mac | NOTE | Mar 13 2025 |
| R-4.5-linux | NOTE | Mar 13 2025 |
| R-4.4-win | NOTE | Mar 13 2025 |
| R-4.4-mac | NOTE | Mar 13 2025 |
| R-4.4-linux | NOTE | Mar 13 2025 |
| R-4.3-win | NOTE | Mar 13 2025 |
| R-4.3-mac | NOTE | Mar 13 2025 |
Exports:computeChiSquaredTestcomputeMultivariateBinaryMatrixcomputeMultivariateDigitizationcomputeMultivariateSupportcomputeQuantileMatrixcomputeUnivariateDigitizationcomputeUnivariateSupportcomputeUnivariateTernaryMatrixfindMultivariateGammaWithSupportfindUnivariateGammaWithSupport
Dependencies:abindaskpassBiobaseBiocGenericscrayoncurlDelayedArraygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| ER positive or negative status of breast tumor samples | breastTCGA_ER |
| Normal or Tumor status of breast samples | breastTCGA_Group |
| Gene expression for 260 genes in 887 breast samples | breastTCGA_Mat |
| Compute chi-squared test | computeChiSquaredTest |
| Compute the binary matrix with digitized divergence coding | computeMultivariateBinaryMatrix |
| Perform binary digitization | computeMultivariateDigitization |
| Estimate the baseline support | computeMultivariateSupport |
| Compute quantile transformations | computeQuantileMatrix |
| Perform ternary digitization | computeUnivariateDigitization |
| Estimate the baseline support | computeUnivariateSupport |
| Compute the ternary matrix with digitized divergence coding | computeUnivariateTernaryMatrix |
| Find optimal gamma and corresponding support for list of feature sets | findMultivariateGammaWithSupport |
| Search for optimal gamma and associated support | findUnivariateGammaWithSupport |
| Cancer Hallmark gene sets from the MSigDB collection | msigdb_Hallmarks |