fcoex

FCBF-based Co-Expression Networks for Single Cells

Bioconductor version: Release (3.17)

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>

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

Installation

To install this package, start R (version "4.3") 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")

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

Details

biocViews	GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, SingleCell, Software, Transcriptomics, mRNAMicroarray
Version	1.13.0
In Bioconductor since	BioC 3.10 (R-3.6) (4 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
Linking To
Suggests	testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData, scater, schex, gridExtra, scran, Seurat, knitr, rmarkdown
System Requirements
Enhances
URL

Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	fcoex_1.13.0.tar.gz
Windows Binary	fcoex_1.13.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	fcoex_1.13.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fcoex
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/fcoex
Bioc Package Browser	https://code.bioconductor.org/browse/fcoex/
Package Short Url	https://bioconductor.org/packages/fcoex/
Package Downloads Report	Download Stats