Package: biomaRt 2.69.0

Introduction | Wormbase | Phytozome | Version 12 | Version 13 | Session Info

Introduction | Selecting an Ensembl BioMart database and dataset | Step1: Identifying the database you need | Step 2: Choosing a dataset | Ensembl mirror sites | Using archived versions of Ensembl | Using Ensembl Genomes | How to build a biomaRt query | Searching for filters and attributes | Using predefined filter values | Finding out more information on filters | filterType | Attribute Pages | Using select() | Result Caching | biomaRt helper functions | exportFASTA | Examples of biomaRt queries | Annotate a set of Affymetrix identifiers with HUGO symbol and chromosomal locations of corresponding genes | Annotate a set of EntrezGene identifiers with GO annotation | Retrieve all HUGO gene symbols of genes that are located on chromosomes 17,20 or Y, and are associated with specific GO terms | Annotate set of idenfiers with INTERPRO protein domain identifiers | Select all Affymetrix identifiers on the hgu133plus2 chip and Ensembl gene identifiers for genes located on chromosome 16 between basepair 1100000 and 1250000. | Retrieve all EntrezGene identifiers and HUGO gene symbols of genes which have a "MAP kinase activity" GO term associated with it. | Given a set of EntrezGene identifiers, retrieve 100bp upstream promoter sequences | Retrieve all 5' UTR sequences of all genes that are located on chromosome 3 between the positions 185,514,033 and 185,535,839 | Retrieve protein sequences for a given list of EntrezGene identifiers | Retrieve known SNPs located on the human chromosome 8 between positions 148350 and 148400 | Given the human gene TP53, retrieve the human chromosomal location of this gene and also retrieve the chromosomal location and RefSeq id of its homolog in mouse. | Connection troubleshooting | r BiocStyle::Biocpkg("biomaRt") specific solutions | Global connection settings | Error: "SSL certificate problem" | Error: "sslv3 alert handshake failure" | Session Info