API for ropensci/biomartr
Genomic Data Retrieval
| Global functions | |
|---|---|
| N50 | Source code |
| assemblies_info_path | Source code |
| assembly_summary_and_rest_status | Source code |
| biomart | Man page Source code |
| biomart_base_urls | Source code |
| biomart_base_urls_select | Source code |
| biomart_full_url | Source code |
| biomartr | Man page |
| biomartr-package | Man page |
| cachedir | Man page Source code |
| cachedir_set | Man page Source code |
| check_annotation_biomartr | Man page Source code |
| check_if_tidy_exists | Source code |
| clean.str.brackets | Source code |
| clean_species_names_helper | Source code |
| collection_table | Source code |
| connected.to.internet | Source code |
| custom_download | Source code |
| custom_download_check_local | Source code |
| db_hosts | Source code |
| docFile | Source code |
| docFile_ncbi_metagenome | Source code |
| done_organisms_bioset_file | Source code |
| download.database | Man page Source code |
| download.database.all | Man page Source code |
| ensembl_all_releases | Source code |
| ensembl_assembly_hits | Source code |
| ensembl_assembly_stem | Source code |
| ensembl_current_release | Source code |
| ensembl_divisions | Man page Source code |
| ensembl_divisions_short | Source code |
| ensembl_download_post_processing | Source code |
| ensembl_fix_wrong_naming | Source code |
| ensembl_ftp_server_url | Source code |
| ensembl_ftp_server_url_fasta | Source code |
| ensembl_ftp_server_url_format | Source code |
| ensembl_ftp_server_url_format_full | Source code |
| ensembl_ftp_server_url_gtf | Source code |
| ensembl_ftp_server_url_release | Source code |
| ensembl_ftp_server_url_release_style_fasta | Source code |
| ensembl_ftp_server_url_release_style_gtf | Source code |
| ensembl_gtf_local_path | Source code |
| ensembl_proper_organism_name | Source code |
| ensembl_rest_url | Source code |
| ensembl_rest_url_assembly | Source code |
| ensembl_rest_url_species | Source code |
| ensembl_rest_url_species_division | Source code |
| ensembl_seq_file_base | Source code |
| ensembl_seq_local_path | Source code |
| ensembl_summaries_filter | Source code |
| existingOrganisms | Source code |
| existingOrganisms_ensembl | Source code |
| exists.ftp.file | Source code |
| exists.ftp.file.new | Source code |
| ftp_url_ensembl | Source code |
| ftp_url_ensembl_dir | Source code |
| ftp_url_refseq_genbank | Source code |
| genomes_wrong_subset_message | Source code |
| get.ensembl.info | Man page Source code |
| getAssemblyStats | Man page Source code |
| getAttributes | Man page Source code |
| getBio | Man page Source code |
| getBioSet | Man page Source code |
| getCDS | Man page Source code |
| getCDSSet | Man page Source code |
| getCollection | Man page Source code |
| getCollectionSet | Man page Source code |
| getDatasets | Man page Source code |
| getENSEMBL | Man page Source code |
| getENSEMBL.Annotation | Source code |
| getENSEMBL.Seq | Man page Source code |
| getENSEMBL.gtf | Man page Source code |
| getENSEMBLGENOMES.Annotation | Source code |
| getENSEMBLGENOMES.Seq | Source code |
| getENSEMBLGENOMES.gtf | 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 |
| getGFFSet | Man page Source code |
| getGO | Man page Source code |
| getGTF | Man page Source code |
| getGenome | Man page Source code |
| getGenomeSet | Man page Source code |
| getGroups | Man page Source code |
| getKingdomAssemblySummary | Man page Source code |
| getKingdomEnsembl | Source code |
| getKingdomGenbank | Source code |
| getKingdomRefseq | 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 |
| getProteomeSet | Man page Source code |
| getRNA | Man page Source code |
| getRNASet | Man page Source code |
| getReleases | Man page Source code |
| getRepeatMasker | Man page Source code |
| getSubMarts | Source code |
| getSummaryFile | Man page Source code |
| getTMPFile | Source code |
| getUniProtInfo | Man page Source code |
| getUniProtSTATS | Man page Source code |
| getUniProtSeq | Source code |
| get_collection_id | Source code |
| get_file_refseq_genbank | Source code |
| gunzip_and_check | Source code |
| is.ensembl.alive | Source code |
| is.genome.available | Man page Source code |
| is.genome.available.ensembl | Source code Source code |
| is.genome.available.refseq.genbank | Source code |
| is.genome.available.uniprot | Source code |
| is.taxid | Source code 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 |
| listNCBIDatabases | Man page |
| local_path_ensembl | Source code |
| local_path_refseq_genbank | Source code |
| lower_cap_underscore_organism_name | Source code |
| make_summary_doc_set | Source code |
| mark_as_complete_set | Source code |
| md5_sum_test | 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 |
| organism_no_hit_message_more_than_one | Source code Source code |
| organism_no_hit_message_zero | Source code Source code |
| please_cite_biomartr | Source code |
| readAssemblyDoc | Source code |
| read_all_kingdoms_assemblies_info | Source code |
| read_all_kingdoms_assemblies_info_fast | 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_md5file | Source code |
| read_proteome | Man page Source code |
| read_rm | Man page Source code |
| read_rna | Man page Source code |
| read_uniprot_info | Source code |
| refseqOrganisms | Man page Source code |
| refseq_genbank_blast_ftp_server_url_blast | Source code |
| refseq_genbank_blast_ftp_server_url_blast_db | Source code |
| refseq_genbank_blast_ftp_server_url_blast_db_md5 | Source code |
| refseq_genbank_download_post_processing | Source code |
| refseq_genbank_ftp_server_kingdoms_url | Source code |
| refseq_genbank_ftp_server_url | Source code |
| refseq_genbank_ftp_server_url_genome | Source code |
| refseq_genbank_ftp_server_url_genome_specific | Source code |
| refseq_genbank_ftp_server_url_genome_specific_summary | Source code |
| refseq_genbank_ftp_server_url_metagenome_specific | Source code |
| refseq_genbank_genome_report_url | Source code |
| refseq_kingdoms_url | Source code |
| select_assembly_refseq_genbank | Source code |
| setTMPFile | Source code |
| summary_cds | Man page Source code |
| summary_genome | Man page Source code |
| supported_biotypes | Source code |
| test | Source code |
| test_url_status | Source code |
| tidy_name | Source code |
| tidy_name2 | Source code |
| toupper_first_char | Source code |
| uniprot_stats_url | Source code |
| validate_release | Source code |
| write_assembly_docs_ensembl | Source code |
| write_uniprot_info | Source code |
| wrong_mart_message | Source code |
