biomartr: Genomic Data Retrieval
Version 0.4.0

Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) ) allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) ), 'NCBI nr', 'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) ) as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

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AuthorHajk-Georg Drost
Date of publication2017-03-14 06:58:21
MaintainerHajk-Georg Drost <hgd23@cam.ac.uk>
LicenseGPL-3
Version0.4.0
URL https://github.com/HajkD/biomartr
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("biomartr")

Man pages

biomart: Main BioMart Query Function
download.database: Download a NCBI Database to Your Local Hard Drive
download.database.all: Download all elements of an NCBI databse
getAssemblyStats: Genome Assembly Stats Retrieval
getAttributes: Retrieve All Available Attributes for a Specific Dataset
getCDS: Coding Sequence Retrieval
getDatasets: Retrieve All Available Datasets for a BioMart Database
getENSEMBLGENOMESInfo: Retrieve ENSEMBLGENOMES info file
getENSEMBLInfo: Retrieve ENSEMBL info file
getFilters: Retrieve All Available Filters for a Specific Dataset
getGenome: Genome Retrieval
getGENOMEREPORT: Retrieve NCBI GENOME_REPORTS file
getGFF: Genome Annotation Retrieval
getGO: Gene Ontology Query
getGroups: Retrieve available groups for a kingdom of life
getKingdomAssemblySummary: Retrieve and summarise the assembly_summary.txt files from...
getKingdoms: Retrieve available kingdoms of life
getMarts: Retrieve All Available BioMart Databases
getMetaGenomeAnnotations: Retrieve annotation *.gff files for metagenomes from NCBI...
getMetaGenomes: Retrieve metagenomes from NCBI Genbank
getMetaGenomeSummary: Retrieve the assembly_summary.txt file from NCBI genbank...
getProteome: Proteome Retrieval
getSummaryFile: Helper function to retrieve the assembly_summary.txt file...
is.genome.available: Check Genome Availability
listDatabases: Retrieve a List of Available NCBI Databases for Download
listGenomes: List All Available Genomes
listGroups: List number of available genomes in each group
listKingdoms: List number of available genomes in each kingdom of life
listMetaGenomes: List available metagenomes on NCBI Genbank
meta.retrieval: Perform Meta-Genome Retieval
meta.retrieval.all: Perform Meta-Genome Retieval of all organisms in all kingdoms...
organismAttributes: Retrieve Biomart Attributes for an Organism
organismBM: Retrieve Biomart Marts and Datasets for an Organism
organismFilters: Retrieve Biomart Filters for an Organism
read_assemblystats: Import Genome Assembly Stats File
read_cds: Import CDS as Biostrings or data.table object
read_genome: Import Genome Assembly as Biostrings or data.table object
read_gff: Import GFF File
read_proteome: Import Proteome as Biostrings or data.table object
refseqOrganisms: Retrieve All Organism Names Stored on refseq

Functions

biomart Man page Source code
clean.str.brackets Source code
connected.to.internet Source code
docFile Source code
download.database Man page Source code
download.database.all Man page Source code
exists.ftp.file Source code
get.ensembl.info Source code
get.ensemblgenome.info Source code
getAssemblyStats Man page Source code
getAttributes Man page Source code
getCDS Man page Source code
getDatasets Man page Source code
getENSEMBL.Annotation Source code
getENSEMBL.Seq Source code
getENSEMBLGENOMES.Annotation Source code
getENSEMBLGENOMES.Seq Source code
getENSEMBLGENOMESInfo Man page Source code
getENSEMBLInfo Man page Source code
getFilters Man page Source code
getGENOMEREPORT Man page Source code
getGFF Man page Source code
getGO Man page Source code
getGenome Man page Source code
getGroups Man page Source code
getKingdomAssemblySummary Man page Source code
getKingdoms Man page Source code
getMarts Man page Source code
getMetaGenomeAnnotations Man page Source code
getMetaGenomeSummary Man page Source code
getMetaGenomes Man page Source code
getProteome Man page Source code
getSubMarts Source code
getSummaryFile Man page Source code
getTMPFile Source code
is.ensembl.alive Source code
is.ensemblgenomes.alive Source code
is.genome.available Man page Source code
listDatabases Man page Source code
listGenomes Man page Source code
listGroups Man page Source code
listKingdoms Man page Source code
listMetaGenomes Man page Source code
meta.retrieval Man page Source code
meta.retrieval.all Man page Source code
organismAttributes Man page Source code
organismBM Man page Source code
organismFilters Man page Source code
read_assemblystats Man page Source code
read_cds Man page Source code
read_genome Man page Source code
read_gff Man page Source code
read_proteome Man page Source code
refseqOrganisms Man page Source code
setTMPFile Source code
test Source code
toupper_first_char Source code

Files

inst
inst/CITATION
inst/seqs
inst/seqs/ortho_thal_aa.fasta
inst/seqs/ortho_lyra_cds.fasta
inst/seqs/ortho_lyra_aa.fasta
inst/doc
inst/doc/MetaGenome_Retrieval.html
inst/doc/Database_Retrieval.R
inst/doc/Introduction.Rmd
inst/doc/Functional_Annotation.Rmd
inst/doc/Sequence_Retrieval.html
inst/doc/BioMart_Examples.html
inst/doc/Database_Retrieval.Rmd
inst/doc/Introduction.R
inst/doc/MetaGenome_Retrieval.R
inst/doc/Sequence_Retrieval.R
inst/doc/BioMart_Examples.Rmd
inst/doc/Database_Retrieval.html
inst/doc/Introduction.html
inst/doc/Sequence_Retrieval.Rmd
inst/doc/Functional_Annotation.R
inst/doc/Functional_Annotation.html
inst/doc/BioMart_Examples.R
inst/doc/MetaGenome_Retrieval.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test-getAttributes.R
tests/testthat/test-getGO.R
tests/testthat/test-organismFilters.R
tests/testthat/test-getMarts.R
tests/testthat/test-getFilters.R
tests/testthat/test-getKingdoms().R
tests/testthat/test-getDatasets.R
tests/testthat/test-getGFF.R
tests/testthat/test-getGroups().R
tests/testthat/test-organismBM.R
tests/testthat/test-is.genome.available.R
tests/testthat/test-getGenome.R
tests/testthat/test-biomart.R
tests/testthat/test-download.database.R
tests/testthat/test-getCDS.R
tests/testthat/test-organismAttributes.R
tests/testthat/test-getProteome.R
NAMESPACE
NEWS.md
R
R/read_gff.R
R/getENSEMBL.Seq.R
R/getKingdoms.R
R/utils.R
R/getGenome.R
R/organismFilters.R
R/meta.retrieval.R
R/getENSEMBL.Annotation.R
R/organismBM.R
R/getAssemblyStats.R
R/download_database.R
R/getGENOMEREPORT.R
R/getENSEMBLGENOMESInfo.R
R/listMetaGenomes.R
R/is.genome.available.R
R/read_genome.R
R/listDatabases.R
R/is.ensemblgenomes.alive.R
R/getMetaGenomeSummary.R
R/toupper_first_char.R
R/download_database_all.R
R/read_assemblystats.R
R/biomart.R
R/listKingdoms.R
R/getProteome.R
R/getMarts.R
R/getFilters.R
R/getENSEMBLGENOMES.Seq.R
R/is.ensembl.alive.R
R/get.ensembl.info.R
R/getGFF.R
R/getMetaGenomeAnnotations.R
R/listGroups.R
R/getENSEMBLInfo.R
R/getENSEMBLGENOMES.Annotation.R
R/read_cds.R
R/getSummaryFile.R
R/exists.ftp.file.R
R/getDatasets.R
R/getSubMarts.R
R/getGO.R
R/getAttributes.R
R/refseqOrganisms.R
R/connected.to.internet.R
R/listGenomes.R
R/getGroups.R
R/get.ensemblgenome.info.R
R/organismAttributes.R
R/getCDS.R
R/getKingdomAssemblySummary.R
R/meta.retrieval.all.R
R/read_proteome.R
R/getMetaGenomes.R
vignettes
vignettes/Introduction.Rmd
vignettes/Functional_Annotation.Rmd
vignettes/Database_Retrieval.Rmd
vignettes/BioMart_Examples.Rmd
vignettes/Sequence_Retrieval.Rmd
vignettes/MetaGenome_Retrieval.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getGO.Rd
man/biomart.Rd
man/listDatabases.Rd
man/meta.retrieval.Rd
man/getENSEMBLInfo.Rd
man/listKingdoms.Rd
man/listGenomes.Rd
man/getAssemblyStats.Rd
man/getKingdomAssemblySummary.Rd
man/getGroups.Rd
man/listMetaGenomes.Rd
man/read_genome.Rd
man/organismBM.Rd
man/organismFilters.Rd
man/getENSEMBLGENOMESInfo.Rd
man/getFilters.Rd
man/read_gff.Rd
man/download.database.Rd
man/getMetaGenomes.Rd
man/refseqOrganisms.Rd
man/read_proteome.Rd
man/read_cds.Rd
man/organismAttributes.Rd
man/meta.retrieval.all.Rd
man/getDatasets.Rd
man/download.database.all.Rd
man/getGenome.Rd
man/getMarts.Rd
man/is.genome.available.Rd
man/getGFF.Rd
man/getProteome.Rd
man/getGENOMEREPORT.Rd
man/getMetaGenomeAnnotations.Rd
man/listGroups.Rd
man/read_assemblystats.Rd
man/getMetaGenomeSummary.Rd
man/getCDS.Rd
man/getAttributes.Rd
man/getSummaryFile.Rd
man/getKingdoms.Rd
biomartr documentation built on May 19, 2017, 3:52 p.m.