Tag: biomaRt

Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

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deseq2 problem

deseq2 problem 0 Hi I am trying to draw a PCA plot with DESeq2 but somehow I cannot use DESeq2 functions. It is a really simple code i wil be pasting below. > transform <- DESeq2::rlog(eliminated_data, blind = TRUE) Error in (function (classes, fdef, mtable) : unable to find an…

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adRn-s/ukbbgwas – githubhot

Explore SNVs associations with traits of UK BioBank. GWAS study results where made publicly available courtesy of Neale’s Lab on August 1st, 2018. For more information please visit: www.nealelab.is/uk-biobank INSTALL In R: devtools::install_github(“adRn-s/ukbbgwas”). DEV(s) Dependencies Mandatory and optional dependencies can all be handled with bioconda. Here’s a complete YAML specification…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Separate exogenous from endogenous transcripts using Salmon RNAseq DTU

Dear friends, We are trying to use Salmon for DTU analysis. We want to separate exogenous from endogenous transcripts by following this post www.biostars.org/p/443701/ and this paper f1000research.com/articles/7-952 We are focusing on a gene called ASCL1 (endo-ASCL1). We transduced cells with lentiviral vector containing ASCL1 ORF only (Lenti-ASCL1). There should…

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GDCquery_Maf error

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

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subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38

subpopulations available in MafH5.gnomAD.v3.1.1.GRCh38 1 @b14a6f0d Last seen 16 hours ago United States Are subpopulation MAFs available for gnomADv.3.1.1 with any package, like they are in MafDb.gnomAD.r2.1.hs37d5? I’m trying to use Genomic Scores to obtain all variants in a genomic range with MAF in any subpopulation >= cutoff. I tried…

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Bioconductor Package Installation

When I try to install the gtf for hg38 BiocManager::install(“TxDb.Hsapiens.UCSC.hg38.knownGene”) I get the following error: ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.2 (2021-11-01) Installing package(s) ‘TxDb.Hsapiens.UCSC.hg38.knownGene’ Error in readRDS(dest) : error reading from connection Per stackoverflow.com/questions/67455984/getoptionrepos-replaces-bioconductor-standard-repositories-see-reposito I…

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Pathway analysis of RNAseq data using goseq package

Hello, I have finished the RNA seq analysis and I am trying to perform some pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How…

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Ensembl | EMBL-EBI Training

Feedback and help Who is this course for? A knowledge of some genomics is required, and some bioinformatics knowledge would be useful but is not essential.  What will I achieve? By the end of the course you will be able to: Explain what Ensembl is and where the data…

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Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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Workflow Platforms for Systems Genetics

Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…

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Bioconductor – branchpointer

DOI: 10.18129/B9.bioc.branchpointer     Prediction of intronic splicing branchpoints Bioconductor version: Release (3.14) Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs. Author: Beth Signal Maintainer: Beth Signal <b.signal at garvan.org.au> Citation (from within R,…

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nf-core/circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

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Unable to get all Uniprot IDs corresponding to Ensembl ID

Unable to get all Uniprot IDs corresponding to Ensembl ID 1 I want to convert Ensembl gene IDs to Uniprot IDs. I have used the biomaRt package in R and perform the following commands. > ensembl <- useEnsembl(biomart = “genes”, dataset = “hsapiens_gene_ensembl”) > getBM(mart=ensembl,attributes=c(“ensembl_gene_id”,”uniprot_gn_id”),filters=”ensembl_gene_id”,values=”ENSG00000183955″,uniqueRows=TRUE); As a result, the following…

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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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Where can I find an annotation table for human gencode ensemble gene ids to gene name/description?

Where can I find an annotation table for human gencode ensemble gene ids to gene name/description? 1 BioMart –> Ensembl Genes –> Human Genes –> Attributes (in left column) –> Select Gene Stable ID, Gene Name, Gene Description (or anything else you want, right pane) –> Hit Count –> 68005…

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identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE

GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE 1 @mikhail-dozmorov-23744 Last seen 1 day ago United States Hi,The GenomicFeatures::makeTxDbFromUCSC function fails with: library(GenomicFeatures) > hg19.refseq.db <- makeTxDbFromUCSC(genome=”hg19″, table=”refGene”) Download the refGene table … Error in .fetch_UCSC_txtable(genome(session), tablename, transcript_ids = transcript_ids) : identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE OK The…

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From where to get a comprehensive list of genes with gene start, gene end and chromosome for build 37?

From where to get a comprehensive list of genes with gene start, gene end and chromosome for build 37? 0 Hi all, I am trying to annotate list of genes with gene start, gene end (build37) and chromosome. I mapped most of the genes from a list downloaded from Biomart/UCSC,…

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Design formula in DESeq2

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

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Help needed for Ensembl Gene ID conversion for RNA-seq data

Hello All, I am new to the RNA-seq world and especially new to the bioinformatics side. We recently completed a RNA-seq experiment (total RNAs) on human samples and we used illumina’s Dragen RNA pipeline which generated salmon gene count (.sf) output files. In the files, the gene ID is in…

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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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Bioconductor – rgsepd

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see rgsepd. Gene Set Enrichment / Projection Displays Bioconductor version: 3.4 R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs

Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs 0 I have a set of 58000 SNPs for which the SNP ID is in the format of: chr:pos:effect allele:ref allele (Grch37 build), but I need to convert this to rsID where one is available for the SNP. I’ve tried using…

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Getting exon sequences for all human genes

Getting exon sequences for all human genes 2 Hi everyone, I would be very grateful if you could help me. I want to download the sequences of all the exons for each human gene. I went to ensembl biomart and tried to do it for BRCA2 first (this was a…

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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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Bioconductor – PPInfer

DOI: 10.18129/B9.bioc.PPInfer     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see PPInfer. Inferring functionally related proteins using protein interaction networks Bioconductor version: 3.12 Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated…

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Convert between UCSC gene id(?) and gene symbol with bioconductor

Convert between UCSC gene id(?) and gene symbol with bioconductor 0 I would like to convert between what I think are UCSC gene ids and gene symbols (see example below). I would prefer to do this with a bioconductor annotation package (org.Hs.eg.db) rather than biomart. Is “UCSC gene id” the…

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What is the Rfam version on Biomart Ensembl?

What is the Rfam version on Biomart Ensembl? 0 Hi all, To enhance RNAseq annotation I would like to use Rfam. I encountered two different version of Rfam on Biomart and on RNAcentral. For the Rfam on RNAcentral I could find that the current version is 14.2, but the version…

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Bioconductor – conclus

DOI: 10.18129/B9.bioc.conclus     ScRNA-seq Workflow CONCLUS – From CONsensus CLUSters To A Meaningful CONCLUSion Bioconductor version: Release (3.13) CONCLUS is a tool for robust clustering and positive marker features selection of single-cell RNA-seq (sc-RNA-seq) datasets. It takes advantage of a consensus clustering approach that greatly simplify sc-RNA-seq data analysis…

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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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How to map old Ensembl Gene IDs to HGNC symbols and Entrez IDs

How to map old Ensembl Gene IDs to HGNC symbols and Entrez IDs 0 I have a list of Ensembl version 74 gene IDs that I need to convert to HGNC symbols. I was wondering what the best way to go about this would be? Originally I used biomaRt with…

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What is the Rfam version on Biomart?

What is the Rfam version on Biomart? 0 Hi all, To enhance RNAseq annotation I would like to use Rfam. I encountered two different version of Rfam on Biomart and on RNAcentral. For the Rfam on RNAcentral I could find that the current version is 14.2, but the version info…

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Easy Way To Get 3′ Utr Lengths Of A List Of Genes

Easy Way To Get 3′ Utr Lengths Of A List Of Genes 4 Hi, as the title says really, I’m wondering if there is any tool available that would allow me to drop in a list of say entrez gene ids and get their corresponding 3′ UTR lenghts? Thanks for…

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tool or database to convert Gene ID to genomic position

tool or database to convert Gene ID to genomic position 1 Hello.I have lots of Pseudogene IDs like LOC100431174 but none of the below methods worked for me to find their genomic position “offline”. I need a table or package to do it offline without querying to a webpage.methods I…

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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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Bioconductor Forum

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…

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Annotation Forge Error: makeOrgPackageFromNCBI

Annotation Forge Error: makeOrgPackageFromNCBI 0 Hi, I just run a code inherited from a recent nature paper: github.com/RoundLab/Ost_CandidaRNASeq However, I got a lot of errors with annotation forge. Would you please help me? Yesterday, I had another error. Today I have rerun it, and I got another error. 🙁 library(“biomaRt”)…

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Looking up Gene IDs in R

Looking up Gene IDs in R 1 Hello, Given a list of gene names, I need to create a table containing the Ensemble ID, chromosome, start, end of that gene. Example: ## ens_id gene view chr start end ## 1: ENSG00000243485 MIR1302-2HG Gene Expression chr1 29553 30267 ## 2: ENSG00000237613…

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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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Biostar Systems

Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 That is good to know that it isn’t just my set of reads…still concerning, though. Comment: STAR vs Novoalign IGV Browser visualization by chasem &utrif; 10 I was not expecting this — not sure what to make of it…

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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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Functional enrichment analysis of bacteria

Functional enrichment analysis of bacteria 2 Hello, I have gene lists from an RNA-seq experiment from E.coli bacteria. So far, I have only worked with model organisms, which are supported by biomaRt, so conversion of gene IDs and functional enrichment analysis within R was easy. Now that I am working…

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Why does Txdb transcript length not always match to transcript end-start position?

Why does Txdb transcript length not always match to transcript end-start position? 2 I have just found an example that biomart’s transcript_length is not identical with transcript_end – transcript_start. ensembl_gene_id mgi_symbol chromosome_name strand start_position end_position gene_biotype transcript_start transcript_end strand.1 transcript_length 128537 ENSMUSG00000037860 Aim2 1 1 173178445 173293606 protein_coding 173178445 173293606…

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Highly used R packages with no Python equivalent

The biggies are obviously DESeq2, limma and edgeR, but they are massive packages doing some very complex statistics, and also have dependency trees that would need to be considered. Depending on your background, you might want to look into the rtracklayer/GenomicRanges eco-system. While I personally am not a fan, I…

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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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