fcoex

DOI: 10.18129/B9.bioc.fcoex    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see fcoex.

FCBF-based Co-Expression Networks for Single Cells

Bioconductor version: 3.15

The fcoex package implements an easy-to use interface to co-expression analysis based on the FCBF (Fast Correlation-Based Filter) algorithm. it was implemented especifically to deal with single-cell data. The modules found can be used to redefine cell populations, unrevel novel gene associations and predict gene function by guilt-by-association. The package structure is adapted from the CEMiTool package, relying on visualizations and code designed and written by CEMiTool's authors.

Author: Tiago Lubiana [aut, cre], Helder Nakaya [aut, ths]

Maintainer: Tiago Lubiana <tiago.lubiana.alves at usp.br>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("fcoex")

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("fcoex")

 

HTML	R Script	fcoex: co-expression for single-cell data
HTML	R Script	fcoex: co-expression for single-cell data integrated with Seurat
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, SingleCell, Software, Transcriptomics, mRNAMicroarray
Version	1.10.0
In Bioconductor since	BioC 3.10 (R-3.6) (3 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	FCBF, parallel, progress, dplyr, ggplot2, ggrepel, igraph, grid, intergraph, stringr, clusterProfiler, data.table, grDevices, methods, network, scales, sna, utils, stats, SingleCellExperiment, pathwayPCA, Matrix
LinkingTo
Suggests	testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData, scater, schex, gridExtra, scran, Seurat, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	fcoex_1.10.0.tar.gz
Windows Binary	fcoex_1.10.0.zip
macOS Binary (x86_64)	fcoex_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fcoex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/fcoex
Package Short Url	https://bioconductor.org/packages/fcoex/
Package Downloads Report	Download Stats