README.md

In Siggers-Lab/hTF_array: Process and Visualize CoRec Data

CoRec

CoRec (short for Cofactor Recruitment) is a protein binding microarray (PBM) based approach for profiling transcription cofactor (COF) recruitment to particular DNA sequences. This package provides tools for analyzing and visualizing the data from CoRec experiments.

Installation

The CoRec package requires a minimum R version of 4.1. It also requires an installation of the MEME suite (see "Detecting the MEME Suite" for more information).

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Siggers-Lab/CoRec", build_vignettes = TRUE)

Getting started

The Introduction to CoRec vignette walks through an example CoRec analysis.

library(CoRec)
vignette("CoRec")

Detecting the MEME Suite

The CoRec package depends on the memes package for running motif comparisons. memes is an R wrapper for the MEME suite, and it requires that the MEME suite be installed and findable. See the memes package "Install MEME" vignette for more information.

For BU SCC users, the most convenient way to ensure that memes can find the MEME suite installation is to create or modify a .Renviron file in your home directory and add the following line:

MEME_BIN=/share/pkg.7/meme/5.3.3/install/bin/

Another option is to provide the path every time you run process_corecmotifs() or find_match(), e.g.:

process_corecmotifs(
    meme_path = "/share/pkg.7/meme/5.3.3/install/bin/",
    ...
)

Siggers-Lab/hTF_array documentation built on Feb. 7, 2024, 11:25 p.m.