MOSClip
This is the released version of MOSClip; for the devel version, see MOSClip.
Multi Omics Survival Clip
Bioconductor version: Release (3.23)
Topological pathway analysis tool able to integrate multi-omics data. It finds survival-associated modules or significant modules for two-class analysis. This tool have two main methods: pathway tests and module tests. The latter method allows the user to dig inside the pathways itself.
Author: Paolo Martini [aut, cre]
, Anna Bortolato [aut]
, Anna Tanada [aut]
, Enrica Calura [aut]
, Stefania Pirrotta [aut]
, Federico Agostinis [aut]
Maintainer: Paolo Martini <paolo.martini at unibs.it>
citation("MOSClip")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MOSClip")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MOSClip")| MOSClip | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, GraphAndNetwork, Pathways, Reactome, Regression, Software, StatisticalMethod, Survival |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | AGPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | MultiAssayExperiment, methods, survminer, graph, graphite, AnnotationDbi, checkmate, ggplot2, gridExtra, igraph, pheatmap, survival, RColorBrewer, SuperExactTest, reshape, NbClust, S4Vectors, grDevices, graphics, stats, utils, ComplexHeatmap, FactoMineR, circlize, corpcor, coxrobust, elasticnet, gRbase, ggplotify, qpgraph, org.Hs.eg.db, Matrix |
| System Requirements | |
| URL | https://github.com/CaluraLab/MOSClip/ |
| Bug Reports | https://github.com/CaluraLab/MOSClip/issues |
See More
| Suggests | RUnit, BiocGenerics, MASS, BiocStyle, knitr, EDASeq, rmarkdown, kableExtra, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MOSClip_1.6.0.tar.gz |
| Windows Binary (x86_64) | MOSClip_1.6.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | MOSClip_1.6.0.tgz |
| macOS Binary (sonoma-arm64) | MOSClip_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MOSClip |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MOSClip |
| Bioc Package Browser | https://code.bioconductor.org/browse/MOSClip/ |
| Package Short Url | https://bioconductor.org/packages/MOSClip/ |
| Package Downloads Report | Download Stats |