CHRONOS
This is the released version of CHRONOS; for the devel version, see CHRONOS.
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
Bioconductor version: Release (3.23)
A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.
Author: Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos Balomenos
Maintainer: Panos Balomenos <balomenos at upatras.gr>
citation("CHRONOS")):
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("CHRONOS")
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("CHRONOS")| CHRONOS | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, KEGG, Pathways, Software, SystemsBiology |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.5) |
| Imports | XML, RCurl, RBGL, parallel, foreach, doParallel, openxlsx, igraph, circlize, graph, stats, utils, grDevices, graphics, methods, biomaRt, rJava |
| System Requirements | Java version >= 1.7, Pandoc |
| URL |
See More
| Suggests | RUnit, BiocGenerics, knitr, rmarkdown |
| 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 | CHRONOS_1.40.0.tar.gz |
| Windows Binary (x86_64) | CHRONOS_1.40.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | CHRONOS_1.40.0.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/CHRONOS |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CHRONOS |
| Bioc Package Browser | https://code.bioconductor.org/browse/CHRONOS/ |
| Package Short Url | https://bioconductor.org/packages/CHRONOS/ |
| Package Downloads Report | Download Stats |