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fcoex

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This is the development version of fcoex; for the stable release version, see fcoex.

FCBF-based Co-Expression Networks for Single Cells

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("fcoex")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, SingleCell, Software, Transcriptomics, mRNAMicroarray
Version 1.15.1
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
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Follow Installation instructions to use this package in your R session.

Source Package
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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/
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