tfclassify

An R package for classifying transcription factors into families, subfamilies, and DNA-binding domain classes based on the Lambert et al. 2018 census.

Installation

# install from GitHub
devtools::install_github("ZohebKhan1/tfclassify/tfclassify")

Usage

library(tfclassify)

# classify a vector of genes
genes <- c("SOX2", "NANOG", "POU5F1", "GATA4", "FOXF1")
classify_tfs(genes)

# classify DESeq2 results and filter to significant TFs
sig_tfs <- classify_tfs(
  deseq_results,
  gene_col = "gene_id",
  filter_to_tfs = TRUE,
  log2fc_col = "log2FoldChange",
  log2fc_threshold = 1,
  padj_col = "padj",
  padj_threshold = 0.05
)

# visualize TF family distribution
plot_tf_families(sig_tfs, top_n = 15, exclude_families = "ZNF")

Tutorial

View the full tutorial: https://zohebkhan1.github.io/tfclassify/

Data source

Example data from:

Martinez JL et al. (2024) Transcriptional consequences of trisomy 21 on neural induction. Front Cell Neurosci. 18:1341141. doi:10.3389/fncel.2024.1341141

TF database

TF classifications based on:

Lambert SA et al. (2018) The Human Transcription Factors. Cell 172(4):650-665. doi:10.1016/j.cell.2018.01.029

Dependencies

• tidyverse
• ggplot2
• dplyr
• devtools