Convert ensembl ids to HGNC gene idsNicholas Cooper
ID conversions: convert_custom()- Convert custom database identifiers. convert_icgc()- Convert ICGC identifiers. convert_pcawg()- Convert PCAWG identifiers. convert_tcga()- Convert TCGA identifiers. convert_hm_genes()- Convert human/mouse gene IDs between Ensembl and Hugo Symbol system. ...
## convert to entrez convert.dict <- readRDS(paste(gtex.path, 'gene-convert-dict.rds', sep = '')) dat.mat <- dat.mat[ which(rownames(dat.mat) %in% convert.dict$Ensembl.Gene.ID) ,] # remove rows with no ENSG match rname.match <- match(rownames(dat.mat), convert.dict$Ensembl....
Convert ensembl gene IDs to gene symbolsXi Wangxi.wangnewcastle.edu.au
entrez_id <chr>, #> # ensembl_gene_id <chr>, vega_id <chr>, ucsc_id <chr>, ena <list>, #> # refseq_accession <list>, ccds_id <list>, uniprot_ids <list>, #> # pubmed_id <list>, mgd_id <list>, rgd_id <list>, lsdb <list>, #> # cosmic <chr>, omim_id <list>...
like ID (a unique machine-understandable identifier, which could be accession, etc.), Parent (any other ID), and Name (like gene name). This would also allow for fast indexing or sorting by ID, Parent, or Name, which would also make it easier toextract or process genes or featuresfor...
Convert gene symbols to ensembl gene IDsXi Wangxi.wangnewcastle.edu.au
Convert gene ids to ensembl idsNicholas Cooper
is often subjective. And that's what this project attempts to standardize.Thevcf2mafandmaf2mafscripts leave most of that responsibility toEnsembl's VEP, but allows you to override their "canonical" isoforms, or use a custom ExAC VCF for annotation. Though the most useful feature is theextensi...
ccds_id as in Ensembl for Mus_musculus related gtf filesI named these tags are called multiplicity tags, and they are further classified into two types depending on the number of possible unique values they have. For those with a low number of possible values, thus low cardinality, each of...