biomartr: Genomic Data Retrieval

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) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. Users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.

AuthorHajk-Georg Drost
Date of publication2017-03-14 06:58:21
MaintainerHajk-Georg Drost <hgd23@cam.ac.uk>
LicenseGPL-3
Version0.4.0
https://github.com/HajkD/biomartr

View on CRAN

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
download.database Man page
download.database.all Man page
getAssemblyStats Man page
getAttributes Man page
getCDS Man page
getDatasets Man page
getENSEMBLGENOMESInfo Man page
getENSEMBLInfo Man page
getFilters Man page
getGenome Man page
getGENOMEREPORT Man page
getGFF Man page
getGO Man page
getGroups Man page
getKingdomAssemblySummary Man page
getKingdoms Man page
getMarts Man page
getMetaGenomeAnnotations Man page
getMetaGenomes Man page
getMetaGenomeSummary Man page
getProteome Man page
getSummaryFile Man page
is.genome.available Man page
listDatabases Man page
listGenomes Man page
listGroups Man page
listKingdoms Man page
listMetaGenomes Man page
meta.retrieval Man page
meta.retrieval.all Man page
organismAttributes Man page
organismBM Man page
organismFilters Man page
read_assemblystats Man page
read_cds Man page
read_genome Man page
read_gff Man page
read_proteome Man page
refseqOrganisms Man page

Files

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

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All documentation is copyright its authors; we didn't write any of that.