gtf

R data package that provides gene transfer format files for commonly investigated model organisms in ChIP-seq studies. These files include annotations of both coding and non-coding genes. The .gtf file format is described here: http://www.gencodegenes.org/gencodeformat.html.

gtf is no longer under active development and is deprecated. Please use rtracklayer::readGFF() instead (from Bioconductor).

Installation instructions

You can install the current GitHub version using the devtools package and the following command in R:

if (!require("devtools")) install.packages("devtools")
devtools::install_github("Bohdan-Khomtchouk/gtf")

And then:

library(gtf)

Troubleshooting

Note: Certain older versions of R may prompt you that:

> install_github("Bohdan-Khomtchouk/gtf")
Downloading GitHub repo Bohdan-Khomtchouk/gtf@master
from URL https://api.github.com/repos/Bohdan-Khomtchouk/gtf/zipball/master
Installing gtf
‘BiocInstaller’ must be installed for this functionality.
Would you like to install it?

1: Yes
2: No

Selection: 1
Error in loadNamespace(name) : there is no package called ‘BiocInstaller’
In addition: Warning message:
package ‘BiocInstaller’ is not available (for R version 3.2.1)

In such cases, first do:

source("http://bioconductor.org/biocLite.R")
biocLite("BiocInstaller")