Integrates pathway information into the differential network analysis of two gene expression datasets as described in Grimes, Potter, and Datta (2019) <doi:10.1038/s41598-019-41918-3>. Provides summary functions to break down the results at the pathway, gene, or individual connection level. The differential networks for each pathway of interest can be plotted, and the visualization will highlight any differentially expressed genes and all of the gene-gene associations that are significantly differentially connected.
| Version: | 0.6.4 |
| Depends: | R (≥ 3.6.0) |
| Imports: | Rcpp (≥ 1.0.1), biomaRt, reactome.db, corpcor, igraph, ggplot2, SeqNet, Rdpack, dplyr, tibble, stats, methods, curl, graphics, grDevices, utils |
| LinkingTo: | Rcpp, RcppArmadillo |
| Suggests: | testthat (≥ 2.1.0), knitr, rmarkdown, readr, bc3net, DWLasso, GENIE3, huge, minet |
| Published: | 2020-07-09 |
| Author: | Tyler Grimes and Somnath Datta |
| Maintainer: | Tyler Grimes <tyler.grimes at ufl.edu> |
| License: | GPL-2 | GPL-3 |
| NeedsCompilation: | yes |
| Citation: | dnapath citation info |
| CRAN checks: | dnapath results |
| Reference manual: | dnapath.pdf |
| Vignettes: |
Introduction to dnapath Package datasets |
| Package source: | dnapath_0.6.4.tar.gz |
| Windows binaries: | r-devel: dnapath_0.6.4.zip, r-release: dnapath_0.6.4.zip, r-oldrel: dnapath_0.6.4.zip |
| macOS binaries: | r-release: dnapath_0.6.3.tgz, r-oldrel: not available |
| Old sources: | dnapath archive |
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