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We present 'corto' (Correlation Tool), a simple package to infer gene regulatory networks and visualize master regulators from gene expression data using DPI (Data Processing Inequality) and bootstrapping to recover edges. An initial step is performed to calculate all significant edges between a list of source nodes (centroids) and target genes. Then all triplets containing two centroids and one target are tested in a DPI step which removes edges. A bootstrapping process then calculates the robustness of the network, eventually re-adding edges previously removed by DPI. The algorithm has been optimized to run outside a computing cluster, using a fast correlation implementation. The package finally provides functions to calculate network enrichment analysis from RNA-Seq and ATAC-Seq signatures as described in the article by Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
| Version: | 1.2.4 |
| Depends: | R (≥ 3.6) |
| Imports: | dplyr, gplots, knitr, methods, rmarkdown, parallel, pbapply, plotrix, stats, utils |
| Published: | 2023-12-06 |
| Author: | Federico M. Giorgi [aut, cre], Daniele Mercatelli [ctb], Gonzalo Lopez-Garcia [ctb] |
| Maintainer: | Federico M. Giorgi <federico.giorgi at gmail.com> |
| License: | LGPL-3 |
| NeedsCompilation: | no |
| Citation: | corto citation info |
| CRAN checks: | corto results |
| Reference manual: | corto.pdf |
| Vignettes: |
corto_vignette |
| Package source: | corto_1.2.4.tar.gz |
| Windows binaries: | r-devel: corto_1.2.4.zip, r-release: corto_1.2.4.zip, r-oldrel: corto_1.2.4.zip |
| macOS binaries: | r-release (arm64): corto_1.2.4.tgz, r-oldrel (arm64): corto_1.2.4.tgz, r-release (x86_64): corto_1.2.4.tgz, r-oldrel (x86_64): corto_1.2.4.tgz |
| Old sources: | corto archive |
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