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 package is for version 3.18 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see fcoex.
FCBF-based Co-Expression Networks for Single Cells
Bioconductor version: 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("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
| Reference Manual |
Details
| biocViews | GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, SingleCell, Software, Transcriptomics, mRNAMicroarray |
| Version | 1.16.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 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 |
| System Requirements | |
| URL |
See More
| Suggests | testthat (>= 2.1.0), devtools, BiocManager, TENxPBMCData, scater, schex, gridExtra, scran, Seurat, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/fcoex |
| Source Repository (Developer Access) | git clone [email protected]:packages/fcoex |
| Package Short Url | https://bioconductor.org/packages/fcoex/ |
| Package Downloads Report | Download Stats |