biomartr: Genomic Data Retrieval with R

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Perform meta-genomic data retrieval and functional annotation retrieval with R.

Author
Hajk-Georg Drost
Date of publication
2016-11-22 09:07:00
Maintainer
Hajk-Georg Drost <hgd23@cam.ac.uk>
License
GPL-3
Version
0.2.0
URLs

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
getAttributes
Retrieve All Available Attributes for a Specific Dataset
getCDS
Coding Sequence Retrieval
getDatasets
Retrieve All Available Datasets for a BioMart Database
getFilters
Retrieve All Available Filters for a Specific Dataset
getGenome
Genome Retrieval
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
getSubgroups
Retrieve available subgroups for a kingdom of life
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
listSubgroups
List number of available genomes in each group
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_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

Files in this package

biomartr
biomartr/inst
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/Evolutionary_Transcriptomics.html
biomartr/inst/doc/Introduction.Rmd
biomartr/inst/doc/Functional_Annotation.Rmd
biomartr/inst/doc/Sequence_Retrieval.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/Database_Retrieval.html
biomartr/inst/doc/Introduction.html
biomartr/inst/doc/Sequence_Retrieval.Rmd
biomartr/inst/doc/Evolutionary_Transcriptomics.R
biomartr/inst/doc/Functional_Annotation.R
biomartr/inst/doc/Functional_Annotation.html
biomartr/inst/doc/Evolutionary_Transcriptomics.Rmd
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-getDatasets.R
biomartr/tests/testthat/test-getGFF.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/download_database.R
biomartr/R/getGENOMEREPORT.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/download_database_all.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/getENSEMBLGENOMES.Annotation.R
biomartr/R/read_cds.R
biomartr/R/getSubgroups.R
biomartr/R/getSummaryFile.R
biomartr/R/getDatasets.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/listSubgroups.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/Sequence_Retrieval.Rmd
biomartr/vignettes/Evolutionary_Transcriptomics.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/listKingdoms.Rd
biomartr/man/listGenomes.Rd
biomartr/man/getSubgroups.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/getFilters.Rd
biomartr/man/read_gff.Rd
biomartr/man/download.database.Rd
biomartr/man/getMetaGenomes.Rd
biomartr/man/listSubgroups.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/getMetaGenomeAnnotations.Rd
biomartr/man/listGroups.Rd
biomartr/man/getMetaGenomeSummary.Rd
biomartr/man/getCDS.Rd
biomartr/man/getAttributes.Rd
biomartr/man/getSummaryFile.Rd
biomartr/man/getKingdoms.Rd