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genomes (version 2.16.0)

Genome sequencing project metadata

Description

Collects genome sequencing project data from NCBI

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Version

Version

2.16.0

License

Artistic-2.0

Maintainer

Chris Stubben

Last Published

February 15th, 2017

Functions in genomes (2.16.0)

esearch

Entrez database search
esummary

Entrez database summaries
genomes-plot

Genome table plots by release date
print.genomes

Print genome tables
read.gff

Read a GFF file from NCBI
read.glimmer

Read a Glimmer output file
genomes-summary

Genome table summaries
genomes-update

Genome table updates
einfo

Entrez database information
image2

Display a matrix image
elink

Entrez database links
like

Pattern matching using wildcards
proks

Prokaryotic genomes at NCBI
read.genemark

Read a GeneMark output file
table2

Format and sort a contigency table
virus

Virus genomes at NCBI
euks

Eukaryotic genomes at NCBI
ftpList

List FTP files and directories
ncbiRelease

NCBI revision history
ncbiSubmit

NCBI submission dates
read.prodigal

Read a Prodigal gene finding output file
read.ncbi.ftp

Read files from the NCBI genomes FTP
efetch

Entrez database downloads
doublingTime

Doubling time for genome projects
ncbiNucleotide

NCBI Nucleotide database
ncbiGenome

NCBI Genome links to the Nucleotide database
ncbiTaxonomy

NCBI taxonomy database
plotby

Plot groups of genomes by release date
read.ptt

Read a NCBI protein or RNA feature table
species

Extract the species name
genomes-internal

Internal genomes Functions
genomes-lines

Add lines to a genomes plot
genomes

Introduction to the genomes package
genus

Extract the genus name
ncbiProject

NCBI BioProject database
ncbiPubmed

NCBI PubMed database
year

Parse a date string