fcoex
This package is for version 3.16 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: 3.16
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 "4.2") 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")| 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 | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GraphAndNetwork, ImmunoOncology, Network, NetworkEnrichment, Pathways, RNASeq, SingleCell, Software, Transcriptomics, mRNAMicroarray |
| Version | 1.12.0 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fcoex_1.12.0.tar.gz |
| Windows Binary | fcoex_1.12.0.zip |
| macOS Binary (x86_64) | fcoex_1.12.0.tgz |
| macOS Binary (arm64) | fcoex_1.12.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |