README.md

In csbl-usp/fcoex: FCBF-based Co-Expression Networks for Single Cells

fcoex

A package for FCBF-based coexpression analysis of single cell data.

The fcoex package implements an easy-to use interface to co-expression analysis based on the FCBF (Fast Correlation-Based Filter) algorithm. The package structure is adapted from the CEMiTool package, relying on visualizations and code designed and written by CEMiTool's authors.

Installing the package

Bioconductor

fcoex is now on Bioconductor (https://bioconductor.org/packages/fcoex/)

To install it, just run:`

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

BiocManager::install(version='devel')

BiocManager::install("fcoex")

Development version

It is also possible to install the current, development version from source code using devtools.

Modifications from version on Bioconductor:

• fc@adjacency returned previously a trimmed version of the adjacency matrix. Now it returns a full, weighted adjacency matrix.
• fc@adjacency_trimmed now returns the trimmed adjacency matrix.

install.packages(devtools)
devtools::install_github(repo = "csbl-usp/fcoex", ref="devel")

csbl-usp/fcoex documentation built on Sept. 15, 2021, 7:42 a.m.