virus: Virus genomes at NCBI

In cstubben/genomes2: Genome sequencing project metadata

Description

Viral reference genome sequencing projects at NCBI

Usage

data(virus)

Format

A genomes data frame with the following 13 variables.

acc

BioProject id

name

Organism name

status

Sequencing status

released

First public sequence release

taxid

Taxonomy id

acc

BioProject Accession number

group

Phylum

subgroup

Class level

size

Total length of DNA (Mb)

gc

Percent GC (guanine or cytosine)

host

Natural host of a virus

segments

Number of segments

genes

Number of genes

proteins

Number of proteins

modified

Sequence modification date

Details

Includes only data represented in the RefSeq dataset.

Source

downloaded from ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/viruses.txt

Examples

data(virus)
plot(virus)
summary(virus)
table2(virus$host)
## most common phages
table2(species(grep("phage", virus$name, value=TRUE)))
## Not run: 
# TABLE only includes RefSeq genomes - see ncbiGenome for links
subset(virus, name=="Nipah virus")
ncbiGenome('Nipah virus[ORGN]')

## End(Not run)

cstubben/genomes2 documentation built on May 14, 2019, 12:25 p.m.