FANTOM5humanSamples: List of FANTOM5 human CAGE samples

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

This is a data.frame object that contains information about all human primary cell, cell line and tissue CAGE datasets (988 datasets) produced by FANTOM5 constortium, which are available for import with CAGEr. The list containes all samples published in the main FANTOM5 publication (Forrest et al. Nature 2014) as presented in the Supplementary Table 1. The columns provide the following information:
sample: name/label of individual sample, which can be used as sample argument in the importPublicData function to retrieve specified sample.
type: type of the sample, either "cell line", "primary cell" or "tissue".
description: description of individual sample as provided by the FANTOM5 consortium.
library_id: unique ID of the CAGE library as provided by the FANTOM5 consortium.
data_url: URL to gzip-ed TSS file at online FANTOM5 data resource, which is used by importPublicData to fetch given sample.

Usage

data(FANTOM5humanSamples)

Format

A data.frame object

CAGEr documentation built on Jan. 17, 2021, 2 a.m.