Tag: ENSEMBL ID
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…
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…
Gene duplicate
Gene duplicate 1 Hi there, I am pretty new to single cell RNA seq and I am trying to learn by doing analysis for a data that has been published already. I am using monocle3 and I realized that some Ensembl IDs that are the same and I was wondering…
Evolutionary differentiation of androgen receptor is responsible for sexual characteristic development in a teleost fish
Animals All the procedures and protocols were approved by the Institutional Animal Care and Use Committee of the National Institute for Basic Biology (15A005, 14A003, 13A023, 12A020, 11A028) and Kyushu University (A21-043-0, A19-137-0, A19-137-1, A19-137-2, A29-088-0, A29-088-1, A29-088-2). Japanese medaka (Oryzias latipes) were bred and maintained under artificial reproductive conditions…
Convertion of ENSEMBL id to gene symbol in the form of a vector.
I have results of a functional analysis as a data.frame with the following columns: names(BP) [1] “category” “ID” “Term” “Genes” “adj_pval” The third column is a comma seperated list the genes containing in each GO term given as ENSEMBL id: Genes 1 ENSG00000159618, ENSG00000197471, ENSG00000166928, ENSG00000134539, ENSG00000116824, ENSG00000198821, ENSG00000111796, ENSG00000150045,…
exchange the monocle data with Seurat
exchange the monocle data with Seurat 0 Hi everyone! I am pretty new to single cell RNA seq analysis. I am using monocle 3 for my analysis. the data file that I have downloaded has already normalized data and it was coming with ensembl ID and I was able to…
Ensembl ID to Gene Symbol Converter
Ensembl ID to Gene Symbol Converter 0 I’m trying to convert ensembl gene IDs to gene symbols. The ensembl gene IDs come from human reference file: Homo_sapiens.GRCh38.dna.primary_assembly.fa. I’ve tried using the BioMart tool from ensembl and the BioTools Converter (www.biotools.fr/human/ensembl_symbol_converter), but both tools still give me a lot of blank…
How can I convert Ensembl ID to gene symbol in R?
I tried several R packages (mygene, org.Hs.eg.db, biomaRt, EnsDb.Hsapiens.v79) to convert Ensembl.gene to gene.symbol, and found that the EnsDb.Hsapiens.v79 package / gene database provides the best conversion quality (in terms of being able to convert most of Ensembl.gene to gene.symbol). Install the package if you have not installed by running…
Ensembl ID mapping GRCh37 vs GRCh38
Ensembl ID mapping GRCh37 vs GRCh38 0 I currently have a large list of Ensembl protein IDs (ENSP) that are from GRCh37. I need to map these IDs to the entry name listed on the UniProt website (e.g. ‘CASPE_HUMAN’ ). I am having trouble doing this using the UniProt dataset…
xml – I am trying to importxml from ENSEMBL using xpath copied from Chrome, but it is not working
I want to use google sheet’s IMPORTXML to extract the gene name (SLC3A1) and ensembl ID (ENSG00000138079) from this URL: asia.ensembl.org/Multi/Search/Results?q=SLC3A1;site=ensembl I tried copying xpath from Chrome and also tried deriving it on my own step by step, but I am only getting a #NA. My xpath: /html/body/div[1]/div/div[2]/div[1]/div[1]/div[2]/div[2]/div[4]/div/div/div[2]/div/div/div[3]/div[2]/div[1]/div[2]/div/div/div/div[1]/div/div[2]/span From Chrome:…
How to analyze the differential expression of a gene if it has several ensembl id
How to analyze the differential expression of a gene if it has several ensembl id 0 Hie, I have obtained the differential expressions of genes (from RNA-seq data) in an excel file. I can see one gene has several ensembl ids and I guess the gene is from the haplotype…
r – convert ALL genes from ensembl ID to symbol without NAs
I tried to convert genes with ensembl ID to Symbol I used the “EnsDb.Hsapiens.v86” package using this code: library(“EnsDb.Hsapiens.v86”) mapIds <- mapIds(EnsDb.Hsapiens.v86, keys = genes, keytype = “GENEID”, column = “SYMBOL”) mapIds Results is like that: ENSG00000033327 GAB2 ENSG00000033627 ATP6V0A1 ENSG00000033800 PIAS1 ENSG00000033867 SLC4A7 ENSG00000034063 < NA > ENSG00000034152 MAP2K3…
refseq select id from ENSEMBL id
Sorry for taking so long to respone to this. For the record, something like this would be possible: gene_search <- entrez_search(db = “gene”, term=”ENSG00000116260″) links <- entrez_link(dbfrom=”gene”, db = “nuccore”, id = gene_search$ids) acc_raw <- entrez_fetch(db = “nuccore”, id=links$links$gene_nuccore_refseqrna, rettype=”acc”), cat(acc_raw,”\n”) NM_001004128.3 NM_002826.5 I’m not sure how you’d get down…
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…
Is there a way to find the GWAS traits to a gene programmatically?
Is there a way to find the GWAS traits to a gene programmatically? 0 Hello folks, I would like to use a gene name (e.g. DOCK2) or its ENSEMBL ID as input, and get as output the reported GWAS traits to the respective gene. I did give a look into…
different ID for ‘gene name’ vs ‘gene synonym’ in ENSEMBL.
I’m finding that the a gene name corresponds to different Ensembl IDs depending if it’s a ‘gene name’ or a ‘gene synonym’ in ENSEMBL. my understanding was that ENSEMBL ID were unique. there’s one location on the genome for each of these genes, so im very unclear how they are…
Convert unigene ID to ensembl ID
Convert unigene ID to ensembl ID 3 Hi Is there a way to convert UniGene ID to ensembl id? using python (my preference) or R? some Unigene ID: Hs.509736 Hs.467701 Hs.138860 Hs.124611 Hs.460988 Hs.49787 Hs.412707 Hs.43697 Hs.447458 Hs.436618 Hs.465087 Hs.439552 Hs.183428 Hs.219140 Hs.153863 Hs.181163 Hs.499891 Hs.410037 Hs.519601 Hs.75640 Hs.450230 Hs.133892…
