Important This package is currently unmaintained and hasn't kept
up with changes in UniProt itself. Please use the
UniProt.ws
package instead.
The UniProt.RES package is an R interface to UniProt's Proteins REST API, giving access to key biological data from UniProt and data from Large Scale Studies data mapped to UniProt.
The Proteins REST API provides access to key biological data from UniProt and data from Large Scale Studies data mapped to UniProt. The services provide sequence feature annotations from UniProtKB, variation data from UniProtKB and mapped from Large Scale data sources (1000 Genomes, ExAC and COSMIC), proteomics data mapped from Large Scale sources (PeptideAtlas, MaxQB and EPD) and genome coordinate mappings.
get /proteins get list of UniProt entries get /proteins/{accession} get UniProt entry by accession get /proteins/{accession}/isoforms get UniProt isoform entries from parent normal entry accession get /proteins/{dbtype}:{dbid} get UniProt entries by uniprot cross reference and its id
library("UniProt.REST") ac <- "P27361" acs <- c("P27361", "P38398") UniProtProtein(ac) UniProtProteins(acs) ## works also as UniProtProtein(ac) UniProtProteinIsoforms(ac)
get /variation get variation by search get /variation/{accession} get UniProt variation features by accession
get /features get features of list of UniProt entries. get /features/type/{type} Search for features of given type and search terms. get /features/{accession} get UniProt features by accession
get /antigen Get antigen of list of UniProt accessions. get /antigen/{accession} Get antigens mapped to UniProt by accession
get /proteomics Get proteomics peptides of list of UniProt accessions. get /proteomics/{accession} Get proteomics peptides mapped to UniProt by accession
get /proteomes Search Proteomes get /proteomes/genecentric/{upid} fetch proteome gene centric proteins by proteome upid get /proteomes/proteins/{upid} fetch proteome proteins by proteome upid get /proteomes/{upid} fetch proteome by proteome upid
get /coordinates query for entries with genomic location get /coordinates/{accession} Get Genome Coordinates by accession. get /coordinates/{dbtype}:{dbid} get by database cross reference: Ensembl, CCDS, HGNC or RefSeq get /coordinates/{taxonomy}/{chromosome}:{gstart}-{gend} get genome coordinate by genome locatio
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