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corto - Inference of Gene Regulatory Networks

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>.

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6.51 score 21 stars 51 scripts 448 downloads

aracne.networks - ARACNe-inferred gene networks from TCGA tumor datasets

This package provides access to ARACNe-inferred gene regulatory networks (regulons) from TCGA tumor datasets. The networks are hosted on Zenodo, downloaded on demand and cached locally with BiocFileCache. The package also contains a function to export them into plain-text format.

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experimentdatagenomehomo_sapiens_datacancerdatadatapkg

5.73 score 7 stars 51 scripts

vulcan - VirtUaL ChIP-Seq data Analysis using Networks

Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.

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systemsbiologynetworkenrichmentgeneexpressionchipseq

3.59 score 13 scripts 422 downloads

vulcandata - VirtUaL ChIP-Seq data Analysis using Networks, dummy dataset

This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package.

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experimentdatahomo_sapiens_datacancerdatachipseqdatadatapkg

3.48 score 9 scripts