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corto  

Inference of Gene Regulatory Networks
View on CRAN: Click here


Download and install corto package within the R console
Install from CRAN:
install.packages("corto")

Install from Github:
library("remotes")
install_github("cran/corto")

Install by package version:
library("remotes")
install_version("corto", "1.2.4")



Attach the package and use:
library("corto")
Maintained by
Federico M. Giorgi
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-10-30
Latest Update: 2023-03-28
Description:
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) .
How to cite:
Federico M. Giorgi (2019). corto: Inference of Gene Regulatory Networks. R package version 1.2.4, https://cran.r-project.org/web/packages/corto
Previous versions and publish date:
0.99.10 (2019-10-30 18:00), 1.0.1 (2020-01-28 20:50), 1.0.2 (2020-01-30 13:00), 1.0.5 (2020-03-03 08:00), 1.0.8 (2020-04-09 13:40), 1.1.0 (2020-06-27 06:30), 1.1.2 (2020-10-13 16:10), 1.1.3 (2020-10-23 14:20), 1.1.4 (2021-03-05 17:50), 1.1.6 (2021-05-24 18:20), 1.1.8 (2021-09-14 18:20), 1.1.9 (2021-09-29 18:00), 1.1.10 (2021-10-22 14:40), 1.1.11 (2022-05-23 17:30), 1.2.0 (2023-02-23 00:10), 1.2.2 (2023-03-28 17:00)
Other packages that cited corto R package
View corto citation profile
Other R packages that corto depends, imports, suggests or enhances
Functions, R codes and Examples using the corto R package
Some associated functions: barplot2 . corto . fcor . fisherp . gsea . gsea2 . kmgformat . mra . mraplot . p2r . p2z . plot_gsea . plot_gsea2 . r2p . scatter . scinot . slice . ssgsea . stouffer . textrepel . val2col . wstouffer . z2p . 
Some associated R codes: corto.R . functions.R . gsea.R . mra.R .  Full corto package functions and examples
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