TFactSR

Installation

install.packages("devtools")

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

BiocManager::install("qvalue")

devtools::install_github("afukushima/TFactSR", build_vignettes = TRUE)

Tutorial

browseVignettes("TFactSR")

or see https://afukushima.github.io/TFactSR/

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Version

Install

install.packages('TFactSR')

Monthly Downloads

125

Version

0.99.0

License

GPL-3

Maintainer

Atsushi Fukushima

Last Published

August 31st, 2023

Functions in TFactSR (0.99.0)

TFactSR

TFactSR: A package for identifying critical transcription factors.

calculateFDRBH

calculates FDR by Benjamini and Hochberg method

calculateQvalue

calculates Q-value

example.df

An example result of enrichment analysis

catalog

A list of TF-target genes (TG) in TFactS.

calculateRC

calculates Random Control (RC)

calculateEnrichmentTest

performs enrichment analysis

calculateEvalue

calculates E-value

AtCatalog

A list of TF-target genes (TG) in Arabidopsis thaliana.

calculateTFactS

calculates TFactS

formatET

formats the result of enrichment test (ET)

formatRC

formats the result of Random Control (RC)

DEGs

An example list of DEGs from DEMO data in TFactS.

DEGs39

An example list of 39 DEGs from DEMO data in TFactS.

FASTcalculateRC

calculates Random Control (RC) fastly?

example.list

An example list of result of enrichment analysis

extractTFTG

extracts transcription factor (TF) and target gene (TG) information

GenesUp_SH1H

An example list of 74 DEGs from AtGenExpress stress dataset.