Genome sequencing project metadata


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Documentation for package ‘genomes’ version 2.2.0

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%like% Pattern matching using wildcards
complete Complete microbial genome dates
doublingTime Doubling time for genome projects
efetch Entrez database downloads
einfo Entrez database information
elink Entrez database links
enaExperiment ENA SRA experiment details
enaFiles ENA SRA submitted or fastq files
enaProject ENA projects
enaSRA ENA sequence read archive
enaStudy ENA SRA study details
enaSubmission ENA SRA submission dates
enaTaxonomy ENA taxonomy statistics
esearch Entrez database search
esummary Entrez database summaries
genomes Introduction to the genomes package
genomes-lines Add lines to a genomes plot
genomes-plot Genome table plots by release date
genomes-subset Subset genome tables
genomes-summary Genome table summaries
genomes-update Genome table updates
genus Extract the genus name
image2 Display a matrix image
lenvs Metagenome sequencing projects at NCBI
leuks Eukaryotic genome projects at NCBI
like Pattern matching using wildcards
lines.genomes Add lines to a genomes plot
lproks Microbial genome projects at NCBI
month Parse a date string
ncbiGenome NCBI Genome links to the Nucleotide database
ncbiNucleotide NCBI Nucleotide database
ncbiProject NCBI BioProject database
ncbiPubmed NCBI PubMed database
ncbiRelease NCBI revision history
ncbiSubmit NCBI submission dates
ncbiTaxonomy NCBI taxonomy database
plot.genomes Genome table plots by release date
plotby Plot groups of genomes by release date
print.genomes Print genome tables
pub Complete microbial genome publications
species Extract the species name
sra Microbial SRA samples at the ENA
subset.genomes Subset genome tables
summary.genomes Genome table summaries
table2 Format and sort a contigency table
update.genomes Genome table updates
virus Virus genomes at NCBI
year Parse a date string