TxDb.Ecoli.K12.MG1655

Annotation package for Escherichia coli str. K12, substr. MG1655. Data source: NCBI.

Installation

You can install the development version of TxDb.Ecoli.K12.MG1655 like so:

devtools::install_github('utubun/TxDb.Ecoli.K12.MG1655')

Example

This is a basic example which shows you how to solve a common problem:

library(TxDb.Ecoli.K12.MG1655)

ecotx <- TxDb.Ecoli.K12.MG1655

# show the information related to the build
ecotx

# extract genes, as genomic ranges
gr <- GenomicFeatures::genes(ecotx)

# show extracted ranges
gr

# convert gene ID into transcript names
head(
  (nm <- biomaRt::select(ecotx, names(gr), 'TXNAME', 'GENEID'))
)

More examples

methods(class = class(ecotx))

help(package = 'GenomicFeatures')