Module bioutils::references::ftp [−][src]
Expand description
Downloads the latest Gencode reference files. In addition to functions for downloading reference files, this file includes the gencode file names and base url as an array. Each function downloads a specific file, the most popular being FASTA and GFF/GTF files related to GRCh38 primary assembly or GRCh38 reference chromosomes.
Constants
| FTP_SITE | |
| HUMAN_RELEASE_DIRECTORY | |
| MOUSE_RELEASE_DIRECTORY |
Functions
| download_gencode_vmxx_2wayconspseudos_gff3_gz | Downloads the latest version of gencode.vMxx.2wayconspseudos.gff3.gz |
| download_gencode_vmxx_2wayconspseudos_gtf_gz | Downloads the latest version of gencode.vMxx.2wayconspseudos.gtf.gz |
| download_gencode_vmxx_annotation_gff3_gz | Downloads the latest version of gencode.vMxx.annotation.gff3.gz |
| download_gencode_vmxx_annotation_gtf_gz | Downloads the latest version of gencode.vMxx.annotation.gtf.gz |
| download_gencode_vmxx_basic_annotation_gff3_gz | Downloads the latest version of gencode.vMxx.basic.annotation.gff3.gz |
| download_gencode_vmxx_basic_annotation_gtf_gz | Downloads the latest version of gencode.vMxx.basic.annotation.gtf.gz |
| download_gencode_vmxx_chr_patch_hapl_scaff_annotation_gff3_gz | Downloads the latest version of gencode.vMxx.chr_patch_hapl_scaff.annotation.gff3.gz |
| download_gencode_vmxx_chr_patch_hapl_scaff_annotation_gtf_gz | Downloads the latest version of gencode.vMxx.chr_patch_hapl_scaff.annotation.gtf.gz |
| download_gencode_vmxx_chr_patch_hapl_scaff_basic_annotation_gff3_gz | Downloads the latest version of gencode.vMxx.chr_patch_hapl_scaff.basic.annotation.gff3.gz |
| download_gencode_vmxx_chr_patch_hapl_scaff_basic_annotation_gtf_gz | Downloads the latest version of gencode.vMxx.chr_patch_hapl_scaff.basic.annotation.gtf.gz |
| download_gencode_vmxx_lncrna_transcripts_fa_gz | Downloads the latest version of gencode.vMxx.lncRNA_transcripts.fa.gz |
| download_gencode_vmxx_long_noncoding_rnas_gff3_gz | Downloads the latest version of gencode.vMxx.long_noncoding_RNAs.gff3.gz |
| download_gencode_vmxx_long_noncoding_rnas_gtf_gz | Downloads the latest version of gencode.vMxx.long_noncoding_RNAs.gtf.gz |
| download_gencode_vmxx_metadata_annotation_remark_gz | Downloads the latest version of gencode.vMxx.metadata.Annotation_remark.gz |
| download_gencode_vmxx_metadata_entrezgene_gz | Downloads the latest version of gencode.vMxx.metadata.EntrezGene.gz |
| download_gencode_vmxx_metadata_exon_supporting_feature_gz | Downloads the latest version of gencode.vMxx.metadata.Exon_supporting_feature.gz |
| download_gencode_vmxx_metadata_gene_source_gz | Downloads the latest version of gencode.vMxx.metadata.Gene_source.gz |
| download_gencode_vmxx_metadata_mgi_gz | Downloads the latest version of gencode.vMxx.metadata.MGI.gz |
| download_gencode_vmxx_metadata_pdb_gz | Downloads the latest version of gencode.vMxx.metadata.PDB.gz |
| download_gencode_vmxx_metadata_polya_feature_gz | Downloads the latest version of gencode.vMxx.metadata.PolyA_feature.gz |
| download_gencode_vmxx_metadata_pubmed_id_gz | Downloads the latest version of gencode.vMxx.metadata.Pubmed_id.gz |
| download_gencode_vmxx_metadata_refseq_gz | Downloads the latest version of gencode.vMxx.metadata.RefSeq.gz |
| download_gencode_vmxx_metadata_selenocysteine_gz | Downloads the latest version of gencode.vM\d{2}.metadata.Selenocysteine.gz |
| download_gencode_vmxx_metadata_swissprot_gz | Downloads the latest version of gencode.vMxx.metadata.SwissProt.gz |
| download_gencode_vmxx_metadata_transcript_source_gz | Downloads the latest version of gencode.vMxx.metadata.Transcript_source.gz |
| download_gencode_vmxx_metadata_transcript_supporting_feature_gz | Downloads the latest version of gencode.vMxx.metadata.Transcript_supporting_feature.gz |
| download_gencode_vmxx_metadata_trembl_gz | Downloads the latest version of gencode.vMxx.metadata.TrEMBL.gz |
| download_gencode_vmxx_pc_transcripts_fa_gz | Downloads the latest version of gencode.vMxx.pc_transcripts.fa.gz |
| download_gencode_vmxx_pc_translations_fa_gz | Downloads the latest version of gencode.vMxx.pc_translations.fa.gz |
| download_gencode_vmxx_polyas_gff3_gz | Downloads the latest version of gencode.vMxx.polyAs.gff3.gz |
| download_gencode_vmxx_polyas_gtf_gz | Downloads the latest version of gencode.vMxx.polyAs.gtf.gz |
| download_gencode_vmxx_primary_assembly_annotation_gff3_gz | Downloads the latest version of gencode.vMxx.primary_assembly.annotation.gff3.gz |
| download_gencode_vmxx_primary_assembly_annotation_gtf_gz | Downloads the latest version of gencode.vMxx.primary_assembly.annotation.gtf.gz |
| download_gencode_vmxx_transcripts_fa_gz | Downloads the latest version of gencode.vM26.transcripts.fa.gz |
| download_gencode_vmxx_trnas_gff3_gz | Downloads the latest version of gencode.vMxx.tRNAs.gff3.gz |
| download_gencode_vmxx_trnas_gtf_gz | Downloads the latest version of gencode.vMxx.tRNAs.gtf.gz |
| download_gencode_vxx_2wayconspseudos_gff3_gz | Downloads the latest version of gencode.vxx.2wayconspseudos.gff3.gz |
| download_gencode_vxx_2wayconspseudos_gtf_gz | Downloads the latest version of gencode.vxx.2wayconspseudos.gtf.gz |
| download_gencode_vxx_annotation_gff3_gz | Downloads the latest version of gencode.vxx.annotation.gff3.gz |
| download_gencode_vxx_annotation_gtf_gz | Downloads the latest version of gencode.vxx.annotation.gtf.gz |
| download_gencode_vxx_basic_annotation_gff3_gz | Downloads the latest version of gencode.vxx.basic.annotation.gff3.gz |
| download_gencode_vxx_basic_annotation_gtf_gz | Downloads the latest version of gencode.vxx.basic.annotation.gtf.gz |
| download_gencode_vxx_chr_patch_hapl_scaff_annotation_gff3_gz | Downloads the latest version of gencode.vxx.chr_patch_hapl_scaff.annotation.gff3.gz |
| download_gencode_vxx_chr_patch_hapl_scaff_annotation_gtf_gz | Downloads the latest version of gencode.vxx.chr_patch_hapl_scaff.annotation.gtf.gz |
| download_gencode_vxx_chr_patch_hapl_scaff_basic_annotation_gff3_gz | Downloads the latest version of gencode.vxx.chr_patch_hapl_scaff.basic.annotation.gff3.gz |
| download_gencode_vxx_chr_patch_hapl_scaff_basic_annotation_gtf_gz | Downloads the latest version of gencode.vxx.chr_patch_hapl_scaff.basic.annotation.gtf.gz |
| download_gencode_vxx_lncrna_transcripts_fa_gz | Downloads the latest version of gencode.vxx.lncRNA_transcripts.fa.gz |
| download_gencode_vxx_long_noncoding_rnas_gff3_gz | Downloads the latest version of gencode.vxx.long_noncoding_RNAs.gff3.gz |
| download_gencode_vxx_long_noncoding_rnas_gtf_gz | Downloads the latest version of gencode.vxx.long_noncoding_RNAs.gtf.gz |
| download_gencode_vxx_metadata_annotation_remark_gz | Downloads the latest version of gencode.vxx.metadata.Annotation_remark.gz |
| download_gencode_vxx_metadata_entrezgene_gz | Downloads the latest version of gencode.vxx.metadata.EntrezGene.gz |
| download_gencode_vxx_metadata_exon_supporting_feature_gz | Downloads the latest version of gencode.vxx.metadata.Exon_supporting_feature.gz |
| download_gencode_vxx_metadata_gene_source_gz | Downloads the latest version of gencode.vxx.metadata.Gene_source.gz |
| download_gencode_vxx_metadata_hgnc_gz | Downloads the latest version of gencode.vxx.metadata.HGNC.gz |
| download_gencode_vxx_metadata_pdb_gz | Downloads the latest version of gencode.vxx.metadata.PDB.gz |
| download_gencode_vxx_metadata_polya_feature_gz | Downloads the latest version of gencode.vxx.metadata.PolyA_feature.gz |
| download_gencode_vxx_metadata_pubmed_id_gz | Downloads the latest version of gencode.vxx.metadata.Pubmed_id.gz |
| download_gencode_vxx_metadata_refseq_gz | Downloads the latest version of gencode.vxx.metadata.RefSeq.gz |
| download_gencode_vxx_metadata_selenocysteine_gz | Downloads the latest version of gencode.vxx.metadata.Selenocysteine.gz |
| download_gencode_vxx_metadata_swissprot_gz | Downloads the latest version of gencode.vxx.metadata.SwissProt.gz |
| download_gencode_vxx_metadata_transcript_source_gz | Downloads the latest version of gencode.vxx.metadata.Transcript_source.gz |
| download_gencode_vxx_metadata_transcript_supporting_feature_gz | Downloads the latest version of gencode.vxx.metadata.Transcript_supporting_feature.gz |
| download_gencode_vxx_metadata_trembl_gz | Downloads the latest version of gencode.vxx.metadata.TrEMBL.gz |
| download_gencode_vxx_pc_transcripts_fa_gz | Downloads the latest version of gencode.vxx.pc_transcripts.fa.gz |
| download_gencode_vxx_pc_translations_fa_gz | Downloads the latest version of gencode.vxx.pc_translations.fa.gz |
| download_gencode_vxx_polyas_gff3_gz | Downloads the latest version of gencode.vxx.polyAs.gff3.gz |
| download_gencode_vxx_polyas_gtf_gz | Downloads the latest version of gencode.vxx.polyAs.gtf.gz |
| download_gencode_vxx_primary_assembly_annotation_gff3_gz | Downloads the latest version of gencode.v37.primary_assembly.annotation.gff3.gz Annotation Type | Genomic Regions Included | File Content Description | File Type Comprehensive gene annotation | PRI | It contains the comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions. This is a superset of the main annotation file. | GFF3 |
| download_gencode_vxx_primary_assembly_annotation_gtf_gz | Downloads the latest version of gencode.vxx.primary_assembly.annotation.gtf.gz Annotation Type | Genomic Regions Included | File Content Description | File Type Comprehensive gene annotation | PRI | It contains the comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions. This is a superset of the main annotation file. | GTF |
| download_gencode_vxx_transcripts_fa_gz | Downloads the latest version of gencode.vxx.transcripts.fa.gz |
| download_gencode_vxx_trnas_gff3_gz | Downloads the latest version of gencode.vxx.tRNAs.gff3.gz |
| download_gencode_vxx_trnas_gtf_gz | Downloads the latest version of gencode.vxx.tRNAs.gtf.gz |
| download_grch38_p13_genome_fa_gz | Downloads the latest version of GRCh38.p13.genome.fa.gz |
| download_grch38_primary_assembly_genome_fa_gz | Convenience functions for each file type. Downloads the latest version of GRCh38.primary_assembly.genome.fa.gz Annotation Type | Genomic Regions Included | File Content Description | File Type Genome sequence, primary assembly (GRCh38) | PRI | Nucleotide sequence of the GRCh38 primary genome assembly (chromosomes and scaffolds). The sequence region names are the same as in the GTF/GFF3 files | Fasta |
| download_grcm39_genome_fa_gz | Downloads the latest version of GRCm39.genome.fa.gz |
| download_grcm39_primary_assembly_genome_fa_gz | Downloads the latest version of GRCm39.primary_assembly.genome.fa.gz |
| download_reference_file | |
| search_files |