CrossICC

This package is for version 3.11 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: 3.11

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 [aut, cre] , Qi Zhao [aut]

Maintainer: Yu Sun <suny226 at mail2.sysu.edu.cn>

Citation (from within R, enter citation("CrossICC")):

Installation

To install this package, start R (version "4.0") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CrossICC")
How to use CrossICC? HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BatchEffect, Classification, Clustering, DifferentialExpression, FeatureExtraction, GUI, GeneExpression, GeneSetEnrichment, Microarray, Normalization, Preprocessing, RNASeq, Software, Survival, Visualization
Version 1.2.0
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 CrossICC_1.2.0.tar.gz
Windows Binary CrossICC_1.2.0.zip
macOS 10.13 (High Sierra) CrossICC_1.2.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CrossICC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CrossICC
Bioc Package Browser https://code.bioconductor.org/browse/CrossICC/
Package Short Url https://bioconductor.org/packages/CrossICC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive