Tag: useMart

r – Alternative Biomart Hosts

I am trying to run the following Biomart script (params$species == “rabbit”){ ensembl = useMart(biomart=”ENSEMBL_MART_ENSEMBL”, dataset=”ocuniculus_gene_ensembl”, host=”uswest.ensembl.org“, ensemblRedirect = FALSE) orgSymbols <- unlist(getBM(attributes=”ensembl_gene_id”, mart=ensembl)) mart <- useMart(dataset = “ocuniculus_gene_ensembl”, biomart=”ensembl”, host=”uswest.ensembl.org“) The host keeps timing out – does anyone know another host URL I could use? Thank you Read more…

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gene ID RNAseq

gene ID RNAseq 0 Hi friends How can I get gene numeric ID and hugo ID by R script? what script should I use? I have this but does not give numeric ID and hugo ID. ibrary(biomaRt) library(dplyr) library(tibble) attributeNames <-c(“ensembl_gene_id”,”external_gene_name”,”HGNC_ID”, “chromosome_name”,”description”) filterValues <- rownames(res) Annotations <- getBM(attributes=attributeNames, filters =…

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Error while converting Gene ID to Ensembl IDs

I have a DEGs data frame with Gene IDs. Pic for reference below I am trying to convert the Gene_IDs into Ensembl IDs. I have tried the following methods library(“AnnotationDbi”) library(“org.Hs.eg.db”) res3$ensid = mapIds(org.Hs.eg.db, keys=res3$Gene_ID, column=”ENSEMBL”, keytype = “SYMBOL”, multiVals = “first”) The above code converted most of the gene…

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Get gene names from rs SNP ids

Gene to rs id library(biomaRt) ## It might take long time to process if many genes (>50) in the list. ## hgnc_gene_symbols.txt is the file that has the list of gene symbols one per line. genes <- read.table(“~/hgnc_gene_symbols.txt”) ensembl = useMart(“ensembl”, dataset=”hsapiens_gene_ensembl”) dbsnp = useMart(“snp”, dataset = “hsapiens_snp”) getHGNC2ENSG =…

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where do I find transcript_biotype

where do I find transcript_biotype 1 Hi newbie_r, I am unsure; however, via biomaRt in R, one can generate a master table that has biotypes for Ensembl and RefSeq ‘transcripts’. require(biomaRt) ensembl <- useMart(‘ensembl’, dataset=”hsapiens_gene_ensembl”) annot <- getBM( attributes = c( ‘hgnc_symbol’, ‘ensembl_gene_id’, ‘ensembl_transcript_id’, ‘entrezgene_id’, ‘refseq_mrna’, ‘gene_biotype’), mart = ensembl)…

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Mapping unique GO term description given a specific GO id

Mapping unique GO term description given a specific GO id 0 I have a list of GO ids and I want to find unique term description such that if I provide say 200 GO IDs I will give 200 specific GO terms. The code snippet I am using is given…

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error while using plant ensembl biomart

error while using plant ensembl biomart 2 Hi, I am trying to extract gene ontology term from plant ensembl biomart using the following code: from pybiomart import Server server = Server(host=”http://plants.ensembl.org”) #print server.list_marts() # available marts mart = server[‘plants_mart’] # connecting plants_mart #print mart.list_datasets() # print available datasets dataset =…

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Retrieving phytozome data using the R bioconductor package biomaRt

Short answer is that I think for now you have to bypass some of the biomaRt functions, and create a Mart object yourself. So give this a try: library(biomaRt) phytozomeMart <- new(“Mart”, biomart = “phytozome_mart”, vschema = “zome_mart”, host = “https://phytozome.jgi.doe.gov:443/biomart/martservice”) The rest of your code should work using this…

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Converting mouse Gene IDs to Human while keeping genes that don’t convert

Hi there, I am using bioMart to convert some gene IDs from mouse to human for some data I generated through RNA-seq. I am currently mapping using the following function: convertMouseGeneList <- function(x){ require(“biomaRt”) human = useMart(“ensembl”, dataset = “hsapiens_gene_ensembl”) mouse = useMart(“ensembl”, dataset = “mmusculus_gene_ensembl”) genesV2 = getLDS(attributes =…

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How to search dbSNP using a list of SNPs and retrieve Gene name (hgnc symbol if existing, otherwise just whatever is in there)

How to search dbSNP using a list of SNPs and retrieve Gene name (hgnc symbol if existing, otherwise just whatever is in there) 2 I have a list of 500.000 SNPs from which I want to obtain the gene name. I try to search with biomaRt library(data.table) library(biomaRt) rs <-…

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Where To Find Annotation File For Agilent Microarray?

An easier way that has [probably] only come about since this question was posted is via biomaRt in R. You can build annotation tables for Agilent 4×44 arrays for mouse and human as follows: require(biomaRt) Homo sapiens # agilent_wholegenome_4x44k_v1 mart <- useMart(‘ENSEMBL_MART_ENSEMBL’) mart <- useDataset(‘hsapiens_gene_ensembl’, mart) annotLookup <- getBM( mart…

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