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Questions tagged [biomart]

biomaRt is a Bioconductor package. Interface to BioMart databases (e.g. Ensembl, COSMIC, Wormbase and Gramene)

In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.

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Using spread with duplicate identifiers for rows giving error

My data looks like this: df <- read.table(header = T, text = "GeneID Gene_Name Species Paralogues Domains Functional_Diversity 1234 DDR1 hsapiens 14 2 8.597482 5678 CSNK1E …
Jack Dean
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How to use lapply to count unique values from a list in r

I have asked a similar question on here before about how to count unique values from a dataframe, but I need to use "lapply" instead because the way I used previously doesn't work or I cant get it to work with a list. I have also been told the using…
Jack Dean
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Issue with lapply using biomart

I am trying to use lapply to change the species name when extracting all the human genes. I'm still learning how to use lapply, I cant work out what I'm doing wrong. So far I have: library(biomaRt) I create the marts: ensembl_hsapiens <-…
Jack Dean
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BioMart: Is there a way to easily change the species for all of my code?

Below is a small fraction of my code: library(biomaRt) ensembl_hsapiens <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") hsapien_PC_genes <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"), …
Jack Dean
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Run a loop using values from a list in R

I am new to R programming and I am using the BioMart package to extract gene paralogues for a list of genes. Using the 'genes' vector below is it possible to loop each value individually into the values part of the 'getBM' function then add the…
Jack Dean
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Replacing column names in one data frame with rows from another data frame if adjacent row matches

I am trying to replace the column names of one data frame with the values in another data frame if the adjacent row in that data frame matches. head(df1) ensembl_gene_id mgi_symbol ENSMUSG00000021252 0610007P14Rik ENSMUSG00000007777 …
microliter
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How can I convert gene symbol to Ensembl ID and uniprot_swissprot in R?

I have a list of genes with their P-value and fold change values as a matrix. Symbols Entrez_IDs logFC AveExpr t P.Value adj.P.Val B 7987405 RASGRP1 10125 -9.924e-01 6.937 -5.467e+00 7.496e-07 …
James
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I would like to retrieve proteins sequences from many protein IDs

library(biomaRt) biomart <- "plants_mart" dataset <- "athaliana_eg_gene" mart <- useMart(biomart = biomart, dataset = dataset) protein_ids <- c("AT5G67220.1", "AT1G07110.1", "AT5G39570.1") protein_sequences <- getSequence(id = protein_ids, type…
code_newbie
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Convert Ensemble ID in gene symbol

I want to convert a list of 20K genes from Ensemble ID to gene symbol using R version 4.1.3. I am naive on using R. I tried to download the following packages: "biomaRt" or "org.HS.eg.db", but everytime I get this error message: Installing package…
Pietro Scaduto
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Converting UniProt IDs to NCBI gene ID is incomplete using biomaRt

I have a list of UniProt IDs, and would like to convert them to NCBI (formally Entrez) gene IDs. The code is working 'fine', except for there are a lot of missing values, despite that information being in the online version of the NCBI gene pages…
DrBrush
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biomaRt - NameSpace loading failed

I installed biomaRt after the latest R update and I am having problems. Whenever I try to call library("biomaRt") it gives me the following error: Error in completeSubclasses(classDef2, class1, obj, where) : trying to get slot "subclasses" from…
Alessia
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R one-to-many mappings

The meth.genes is a character vector based on the gene names that correspond with the rownames of the meth dataframe. However, it is a 1-to-many match, whereby one gene can be mapped to multiple rownames in meth. After a series of downstream…
melolili
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error using biomaRt: Error in `mutate()` and `dplyr::select()`

hope you are fine! I am having an error i never had using biomaRt. Here is the code I am using and the error I am seeing: `> library("biomaRt") > # release 88 of Ensembl is March 2017 > #https://www.ensembl.org/info/website/archives/index.html >…
Chiara
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Single Cell RNA seq: top 10 genes

I am very new to single cell rna seq analysis, I used to biomaRt to get my gene names using this code annot<-getBM(c("ensembl_gene_id", "chromosome_name","ensembl_transcript_id", "strand", "start_position",…
Maryam
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How to I convert genes/features of species A to orthologous genes for species B for cross species single cell RNA sequencing dataset integration

I am trying to do a cross-species single cell RNA sequencing integration using Seurat with a zebrafish dataset and a chick dataset. I have generated seurat objects for both. How can I use Ensemble ID (bioMart) to convert chick genes dataset to those…
Sam
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