CrossICC
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CrossICC.
An Interactive Consensus Clustering Framework for Multi-platform Data Analysis
Bioconductor version: 3.13
CrossICC utilizes an iterative strategy to derive the optimal gene set and cluster number from consensus similarity matrix generated by consensus clustering and it is able to deal with multiple cross platform datasets so that requires no between-dataset normalizations. This package also provides abundant functions for visualization and identifying subtypes of cancer. Specially, many cancer-related analysis methods are embedded to facilitate the clinical translation of the identified cancer subtypes.
Author: Yu Sun <suny226 at mail2.sysu.edu.cn>, Qi Zhao <zhaoqi at sysucc.org.cn>
Maintainer: Yu Sun <suny226 at mail2.sysu.edu.cn>
citation("CrossICC")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("CrossICC")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | BatchEffect, Classification, Clustering, DifferentialExpression, FeatureExtraction, GUI, GeneExpression, GeneSetEnrichment, Microarray, Normalization, Preprocessing, RNASeq, Software, Survival, Visualization |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| License | GPL-3 | file LICENSE |
| Depends | R (>= 3.5), MASS |
| Imports | data.table, methods, MergeMaid, ConsensusClusterPlus, limma, cluster, dplyr, Biobase, grDevices, stats, graphics, utils |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, testthat, knitr, shiny, shinydashboard, shinyWidgets, shinycssloaders, DT, ggthemes, ggplot2, pheatmap, RColorBrewer, tibble, ggalluvial |
| 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 | |
| Windows Binary | |
| macOS 10.13 (High Sierra) | |
| Source Repository | git clone https://git.bioconductor.org/packages/CrossICC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/CrossICC |
| Package Short Url | https://bioconductor.org/packages/CrossICC/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.13 | Source Archive |