Package: biomartr 1.0.11

Use Case #1: Functional Annotation of Genes Sharing a Common Evolutionary History | Step 1 | Enrichment Analyses

Topics | Perform Meta-Genome Retrieval | Getting Started | Retrieve Genomic Sequences | Example NCBI RefSeq: | Example NCBI Genbank: | Example ENSEMBL | Retrieval from NCBI RefSeq | Restarting a corrupted download | Un-zipping downloaded files | Retrieval from NCBI Genbank | Retrieval from ENSEMBL | Retrieve groups or subgroups of species | Example retrieval of all Gammaproteobacteria genomes from NCBI RefSeq: | Example retrieval of all Adenoviridae genomes from NCBI RefSeq: | Meta retrieval of genome assembly quality information | Metagenome project retrieval from NCBI Genbank | Retrieve Protein Sequences | Retrieval from NCBI RefSeq: | Retrieval from NCBI Genbank: | Retrieval from ENSEMBL: | Retrieve CDS Sequences | Retrieve GFF files | Retrieve GTF files | Retrieve RNA sequences | Retrieve Repeat Masker Sequences | Retrieve Individual Genomes for all Species in the Tree of Life | Genome Retrieval | Proteome Retrieval

Biological Sequence Retrieval | Topics | Getting Started with Sequence Retrieval | Example NCBI RefSeq (?is.genome.available): | Using the NCBI Taxonomy ID instead of the scientific name to screen for organism availability | Using the accession ID instead of the scientific name or taxid to screen for organism availability | A small negative example | Example NCBI Genbank (?is.genome.available): | Using is.genome.available() with ENSEMBL | Example ENSEMBL (?is.genome.available): | Example UniProt (?is.genome.available): | Listing the total number of available genomes | Retrieving kingdom, group and subgroup information | Analogous computations can be performed for groups and subgroups | Downloading Biological Sequences and Annotations | Genome Retrieval | Example NCBI RefSeq: | Use taxid id for genome retrieval | Use assembly_accession id for genome retrieval | Example NCBI Genbank: | Use taxonomy id for genome retrieval | Example ENSEMBL: | GenomeSet Retrieval | Proteome Retrieval | Example Retrieval Uniprot: | ProteomeSet Retrieval | CDS Retrieval | CDSSet Retrieval | RNA Retrieval | RNASet Retrieval | Retrieve the annotation file of a particular genome | Removing corrupt lines from downloaded GFF files | GFFSet Retrieval | Repeat Masker Retrieval | Genome Assembly Stats Retrieval | Collection Retrieval

Functional Annotation Retrieval from Ensembl Biomart | Getting Started | The old biomaRt query methodology | Extending biomaRt using the new query system of the biomartr package | Getting Started with biomartr | Retrieve marts, datasets, attributes, and filters with biomartr | Retrieve Available Marts | Retrieve Available Datasets from a Specific Mart | Retrieve Available Attributes from a Specific Dataset | Retrieve Available Filters from a Specific Dataset | Organism Specific Retrieval of Information | Construct BioMart queries with biomartr | Gene Ontology | GO Annotation Retrieval via BioMart

Retrieve Sequence Databases from NCBI | Getting Started | List available databases | Download NCBI databases | Example NCBI nr | Example NCBI nt | Example NCBI RefSeq | Example PDB | Example NCBI Taxonomy | Example NCBI Swissprot | Example NCBI CDD Delta