API for HajkD/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
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_download_post_processing 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
HajkD/biomartr documentation built on Dec. 9, 2023, 7:25 p.m.