biomartr: Genomic Data Retrieval with R

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

AuthorHajk-Georg Drost
Date of publication2016-12-15 17:57:34
MaintainerHajk-Georg Drost <hgd23@cam.ac.uk>
LicenseGPL-3
Version0.2.1
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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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