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MOSClip

https://github.com/caluralab/mosclip

Science Score: 39.0%

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    Found 2 DOI reference(s) in README
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    Low similarity (10.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: CaluraLab
  • Language: R
  • Default Branch: main
  • Size: 32 MB
Statistics
  • Stars: 0
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created almost 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

MOSClip

Multi-Omics Survival Clip

MOSClip is a topological pathway analysis tool to test survival association of pathways in a multi-omic framework.

Description

MOSClip R package implements a statistical approach able to integrate multi-omic data and look for survival associated gene modules. It integrates multiple omics - trascriptomics, methylomics, genomic mutations, and genomic copy number variations - using various data dimensionality reduction strategies and multivariate models. Exploiting graph theory, pathways can be decomposed into their connected components, that we call modules. The analysis can then be performed at the level of entire pathways or pathway modules. MOSClip pathway analysis serves two primary purposes: testing the survival association of pathways or modules using the Cox proportional hazard model, and conducting a two-class analysis with a generalized linear model. Additionally, the package offers valuable graphical tools to visualize and interpret the results.

Installation

You can install MOSClip directly from GitHub writing the following commands in your R console.

``` r

Install the package from Bioconductor

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("MOSClip")

Install the package from GitHub

devtools::install_github("CaluraLab/MOSClip")

```

References

Paolo Martini, Monica Chiogna, Enrica Calura, and Chiara Romualdi. 2019. “MOSClip: Multi-Omic and Survival Pathway Analysis for the Identification of Survival Associated Gene and Modules.” Nucleic Acids Research 47 (14): e80. https://doi.org/10.1093/nar/gkz324

Owner

  • Name: Calura Lab
  • Login: CaluraLab
  • Kind: organization
  • Email: enrica.calura@unipd.it
  • Location: Department of Biology, University of Padova, Italy

Computational Cancer Genomics

GitHub Events

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  • Delete event: 1
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  • Create event: 4
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  • Delete event: 1
  • Push event: 10
  • Create event: 4

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Last synced: 10 months ago

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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 2,111 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
bioconductor.org: MOSClip

Multi Omics Survival Clip

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2,111 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 31.5%
Average: 42.4%
Downloads: 95.6%
Maintainers (1)
paolo.martini@unibs.it
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.4.0 depends
  • AnnotationDbi * imports
  • ComplexHeatmap * imports
  • FactoMineR * imports
  • Matrix * imports
  • MultiAssayExperiment * imports
  • NbClust * imports
  • RColorBrewer * imports
  • S4Vectors * imports
  • SuperExactTest * imports
  • checkmate * imports
  • circlize * imports
  • corpcor * imports
  • coxrobust * imports
  • elasticnet * imports
  • gRbase * imports
  • ggplot2 * imports
  • ggplotify * imports
  • grDevices * imports
  • graph * imports
  • graphics * imports
  • graphite * imports
  • gridExtra * imports
  • igraph * imports
  • methods * imports
  • org.Hs.eg.db * imports
  • pheatmap * imports
  • qpgraph * imports
  • reshape * imports
  • stats * imports
  • survival * imports
  • survminer * imports
  • utils * imports
  • BiocGenerics * suggests
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  • EDASeq * suggests
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  • RUnit * suggests
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  • testthat >= 3.0.0 suggests