Tag: useMart

How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?

How to do KEGG pathway analysis when I have a gene with multiple entrez IDs? 0 Hello, I did DESeq2 on my samples and I have a list of DEGs that I would like to do kegg pathway analysis on. For DESeq2 I used biomart and tximport to assign external…

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How to get just protein_coding genes using biomart in R

How to get just protein_coding genes using biomart in R 2 Dear all, I would like to have help with getting just protein_coding genes from gene expression file using biomart. What I have is a file of all genes expression for mouse (mm10) with ensemble gene_names, and I need to…

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map Ensembl gene ID from hg19 to hg38

map Ensembl gene ID from hg19 to hg38 0 Hello! I would like to convert Ensembl gene ID from hg19 to hg38 with R. I tried with this code: ensembl <- useMart(“ensembl”, dataset = “hsapiens_gene_ensembl”, host= “grch37.ensembl.org“) ensembl_ids <- c(“ENSG00000183878”, “ENSG00000146083”) converted_ids <- getLDS(attributes = c(“ensembl_gene_id”), filters = “ensembl_gene_id”, values…

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Hugo_Symbol to Entrez ID

Hello, I have Myeloid-Acute Myeloid Leukemia (AML) RNAseq data file data_mrna_seq_rpkm.csv. This file has Hugo_Symbols for all 22,844 genes but not its Entrez IDs. I was able use to two methods in R programming 1) library(org.Hs.eg.db) mapIDs method and 2) biomaRT method to get the entrez_ID of only 16,569 genes…

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Convert gene id’s to gene symbol preserving gene id’s in deseq2

Convert gene id’s to gene symbol preserving gene id’s in deseq2 0 Good evening, I have a dds object with gene id’s, and I need to convert them into gene symbols. The point is that some genes do not have a match and I don’t want to lose them in…

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DESeq2 results – Annotating and exporting results

Hi, I am working with isoforms.results from RSEM analysis. I am trying to annotate my deseq results with symbol and entrez IDs, following the vignette master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#annotating-and-exporting-results Unfortunately, I cannot export them as a csv file because the 2 elements I am adding are list. do you have any idea how…

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Unsupervised clustering on gene expression data

Clustering is a data mining method to identify unknown possible groups of items solely based on intrinsic features and no external variables. Basically, clustering includes four steps: 1) Data preparation and Feature selection, 2) Dissimilarity matrix calculation, 3) applying clustering algorithms, 4) Assessing cluster assignment I use an RNA-seq dataset…

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Biomart doesnt work in R for big input data. How to run it in Python ?

Biomart doesnt work in R for big input data. How to run it in Python ? 0 I am trying to use Biomart for a list of variants (with rs ids) to retrieve the consequence_types for each variant but as because my file is too big (80621 entries) i am…

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Retrieve only protein coding esnsemble gene ids and gene symbols

Retrieve only protein coding esnsemble gene ids and gene symbols 1 I tried without success different ways to retrieve the current list of ensemble gene ids including the gene symbol for only protein coding genes by using the R library Biomart. Here is the code: library(biomaRt) ensembl = useMart(biomart=”ensembl”, dataset=”hsapiens_gene_ensembl”)…

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Mapping Ensembl Gene IDs with dot suffix

Here’s an example of doing the conversion using biomaRt. You can use the versioned IDs you’ve got, but you’ll see it’s better the remove the version numbers. First, we’ll load biomaRt and use your example IDs. library(biomaRt) mart <- useMart(biomart = “ensembl”, dataset = “hsapiens_gene_ensembl”) gene_ids_version <- c(“ENSG00000236246.1”, “ENSG00000281088.1”, “ENSG00000254526.1”,…

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Convert Human to Mouse Symbols

I’m trying to create a working function that takes a column of human gene symbols as input and outputs a vector of mouse gene symbols that is the same length. (I’m trying to use the function to replace the human genes in a dataframe with mouse genes) I have tried…

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How to process (seems) Agilent microarrry data?

Edit September 5, 2019 NB – this original answer is for 1-colour (channel) Agilent data. Another generic pipeline for 2-colour Agilent is here: A: build the expression matrix step by step from GEO raw data ————— Limma can be used to process Agilent microarray data. Assuming that your data is…

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Comparing gene expression with copy number variation in TCGA

Hello, I want to compare (with a PCA) gene expression against copy number variation at gene level in a TCGA project.When I retrieve the gene expression every value is mapped by sample and gene. But for the copy number variation, I get only chromosomal locations.To do the PCA, I want…

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Seurat scRNA convert Ensembl ID to gene symbol

Hi, I’m download some datasets from Geo Database (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155960) I found the names are in ENSEMBL nomenclature and I need to convert into Gene symbol in order to do the QC metrics in the Seurat pipeline. I’m using this code to convert the ENSEMBL to gene symbol: library(Seurat) library(patchwork) library…

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trouble getting gene names from biomaRt

I have an excel file, which contains columns chrom, pos, id, ref and alt. I want to add a new column, which will have the name of the genes for the corresponding rows. For that I am using getBM() function in biomaRt, but it takes too much time to finish….

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TAIR Gene Symbols

Hey, There are two approaches here. 1, org.At.tair.db You can use the annotation DB packages from Bioconductor, specifically org.At.tair.db. Copying my own answer from here: A: Biomart query returns NA when searching for entrez_id, while manual search works library(org.At.tair.db) genes <- c(“AT2G14610″,”AT4G23700″,”AT3G26830”, “AT3G15950″,”AT3G54830″,”AT5G24105”) keytypes(org.At.tair.db) mapIds(org.At.tair.db, keys = genes, column =…

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Missing Gene Symbols From Mgi With Biomart (Mouse)

Missing Gene Symbols From Mgi With Biomart (Mouse) 1 I’m trying to use biomaRt to get attributes for a bunch of genes. When I try it, I notice that there are some missing values. Can someone tell me why? Ex.: library(biomaRt) mart <- useMart(biomart=”ensembl”, dataset=”mmusculus_gene_ensembl”) results <- getBM(attributes = c(“gene_biotype”,…

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Comment: None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys metho

In that case let us consider your dataframe: “` data = c(“ENST00000003583.12”, “ENST00000003912.7”, “ENST00000008440.9”, “ENST00000009105.5”, “ENST00000010299.10”, “ENST00000011700.10”, “ENST00000037502.11”, “ENST00000040877.2”, “ENST00000054650.8”, “ENST00000054666.11”, “ENST00000054668.5”, “ENST00000060969.5”, “ENST00000072644.7”, “ENST00000078527.8”, “ENST00000164247.5”, “ENST00000166244.8”, “ENST00000167825.5”, “ENST00000194214.9”, “ENST00000196061.5”, “ENST00000207157.7”) “` Remove the numbers after . “` enst <- gsub("\\.[0-9]*$", "", data) “` then follow the command “` library(biomaRt)…

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Answer: None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys metho

You can use bioMart to solve this problem: Let your data be as follows: “` data = c(“ENST00000234590″,”ENST00000295688″,”ENST00000319248″,”ENST00000436427”, “ENST00000458748”, “ENST00000384384”, “ENST00000524851”, “ENST00000530019”, “ENST00000532872”, “ENST00000610851”, “ENST00000618227”, “ENST00000229239”) “` then, “` library(biomaRt) mart <- useMart("ensembl","hsapiens_gene_ensembl") genes <- getBM(attributes=c("ensembl_transcript_id","external_gene_name","ensembl_gene_id"), filters = "ensembl_transcript_id", values = data, mart = mart) rownames(genes) <- genes$ensembl_transcript_id names(genes) =…

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problems annotating a list of DEGs from DESeq2

BiomaRt: problems annotating a list of DEGs from DESeq2 0 @alanghudson-16729 Last seen 11 hours ago United States Hi, I am trying to annotate a list of differentially expressed genes output by DESeq2, with ensembl IDs, gene symbols and gene descriptions. I originally aligned and mapped the reads using a…

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How to extract the DNA sequence 1000 bp around the Transcription start site (TSS) of a gene symbol in NCBI gene with R?

How to extract the DNA sequence 1000 bp around the Transcription start site (TSS) of a gene symbol in NCBI gene with R? 0 I am trying to extract the DNA sequence 1000 bp around the Transcription start site (TSS) of a gene, and I get a code as follows:…

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Getting chromosome of unusual chromosome names e.g. ‘CHR_HSCHR8_8_CTG1’

Getting chromosome of unusual chromosome names e.g. ‘CHR_HSCHR8_8_CTG1’ 0 I made a biomaRt query: library(biomaRt) mart = useMart(‘ensembl’, dataset=”hsapiens_gene_ensembl”) genes = getBM(attributes = c(“chromosome_name”,”start_position”, “hgnc_symbol”, “uniprot_gn_symbol”, “uniprot_gn_id”), mart = mart, values = list(“protein_coding”,c(1:22))) Most of the chromosome_name values are regular numbers 1 to 22. However, some are unusual, such as…

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biomaRt crashes R studio

biomaRt crashes R studio 0 Hey everyone, I just wanted to execute a script that worked before. However, everytime I try to run it now RStudio gets unresponsive. I didn’t change anything. Does anyone else experience this? This is an extract from my script: library(biomaRt) … mart <- useMart(“ENSEMBL_MART_ENSEMBL”) mart…

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Problem with tximport and plasmodium falciparum

Hello, I aligned my samples with kallisto to a transcriptome for plasmodium falciparum. The file I used to make the reference is Plasmodium_falciparum.ASM276v2.cdna.all.fa.gz which I downloaded from here ftp.ensemblgenomes.org/pub/protists/release55/fasta/plasmodium_falciparum/cdna/Plasmodium_falciparum.ASM276v2.cdna.all.fa.gz. However, I am having issues with tximport. The error that I get is: Error in .local(object, …) : None of the…

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Annotating snps with gene information

Annotating snps with gene information 0 Hi, I am trying to annotate a list of snps with the ENSG gene number using biomaRt. I need to use ensemble version 91. I have built the following query: snps = c(“rs201327123” “rs141149254” “rs114420996” “rs62637817″) ensembl.snp = useEnsembl(biomart=”snps”, version=91) mart.snp <- useMart(biomart =…

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get build 37 positions from dbSNP rsIDs

get build 37 positions from dbSNP rsIDs 4 $ mysql –user=genome –host=genome-mysql.cse.ucsc.edu -A -D hg19 -e ‘select chrom,chromStart,chromEnd,name from snp147 where name in (“rs371194064″,”rs779258992″,”rs26″,”rs25”)’ +——-+————+———-+————-+ | chrom | chromStart | chromEnd | name | +——-+————+———-+————-+ | chr7 | 11584141 | 11584142 | rs25 | | chr7 | 11583470 | 11583471…

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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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