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.
This is a data.frame object that contains information about all mouse primary cell, cell line and tissue CAGE datasets (395) 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.
exampleCAGEset
(Package: CAGEr) :
Example CAGEset object with zebrafish CAGE data
This is a CAGEset object that contains CAGE data for part of chromosome 13 from five different zebrafish (Danio rerio) samples. It is intended to be used as an input data in running examples from CAGEr package help pages.
providing 
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