Tag: TAIR

ORA with clusterProfiler

Hello everyone, I am trying to do an enrichment analysis of Arabidopsis data, however I am still wondering how to build it or what to use as a background (universe), could you guide me? I am working with this example. diff_genes <- read_delim(file = “differential_genes.tsv”, delim = “\t”) biomartr::organismBM(organism =…

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annotatePeak error for some problem

annotatePeak error for some problem 0 hello, everyone: when I use ChIPseeker to annotatePeak my chip-seq peaks, some error came. When I use this function, I encounter some issues and would like to seek advice. How can I resolve this problem? I would greatly appreciate your help. my code is…

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Functional annotation with nr database followed by GO enrichment analysis

Functional annotation with nr database followed by GO enrichment analysis 0 Dear Stars, I am working in the field of plant biology. I usually performed functional annotation using Araport database (i.e. Arabidopsis database) After functional annotation, I could perform GO enrichment analysis using R wherein there is library called “Org.At.tair.db”…

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Regulation of gene editing using T-DNA concatenation

Gelvin, S. B. Integration of Agrobacterium T-DNA into the plant genome. Annu. Rev. Genet. 51, 195–217 (2017). Article  CAS  PubMed  Google Scholar  Gelvin, S. B. Plant DNA repair and Agrobacterium T-DNA integration. Int. J. Mol. Sci. doi.org/10.3390/ijms22168458 (2021). Jupe, F. et al. The complex architecture and epigenomic impact of plant…

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GreenLight Biosciences hiring Bioinformatics Scientist (Crop Science) in Triangle, NC

About GreenlightAt GreenLight we are working to solve two of the world’s greatest problems: global food insecurity and equal access to vaccines and the associated health benefits. Unlike most corporations who can be required to put profits ahead of other principles, GreenLight is one of the first Public Benefit Corporations…

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Bioconductor – rrvgo

DOI: 10.18129/B9.bioc.rrvgo     Reduce + Visualize GO Bioconductor version: Release (3.13) Reduce and visualize lists of Gene Ontology terms by identifying redudance based on semantic similarity. Author: Sergi Sayols [aut, cre] Maintainer: Sergi Sayols <sergisayolspuig at gmail.com> Citation (from within R, enter citation(“rrvgo”)): Installation To install this package, start…

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html – SJTUG Mirror Index

.. BSgenome.Amellifera.BeeBase.assembly4.html BSgenome.Amellifera.UCSC.apiMel2.html BSgenome.Athaliana.TAIR.01222004.html BSgenome.Athaliana.TAIR.04232008.html BSgenome.Btaurus.UCSC.bosTau3.html BSgenome.Btaurus.UCSC.bosTau4.html BSgenome.Celegans.UCSC.ce2.html BSgenome.Cfamiliaris.UCSC.canFam2.html BSgenome.Dmelanogaster.UCSC.dm2.html BSgenome.Dmelanogaster.UCSC.dm3.html BSgenome.Drerio.UCSC.danRer5.html BSgenome.Ecoli.NCBI.20080805.html BSgenome.Ggallus.UCSC.galGal3.html BSgenome.Hsapiens.UCSC.hg17.html BSgenome.Hsapiens.UCSC.hg18.html BSgenome.Hsapiens.UCSC.hg19.html BSgenome.Mmusculus.UCSC.mm8.html BSgenome.Mmusculus.UCSC.mm9.html BSgenome.Ptroglodytes.UCSC.panTro2.html BSgenome.Rnorvegicus.UCSC.rn4.html BSgenome.Scerevisiae.UCSC.sacCer1.html BSgenome.Scerevisiae.UCSC.sacCer2.html GGHumanMethCancerPanelv1.db.html GO.db.html Hs6UG171.db.html HuExExonProbesetLocationHg18.html HuExExonProbesetLocationHg19.html HuO22.db.html IlluminaHumanMethylation27k.db.html JazaeriMetaData.db.html KEGG.db.html LAPOINTE.db.html Masks.Dmelanogaster.UCSC.dm3.html MoExExonProbesetLocation.html Mu15v1.db.html Mu22v3.db.html Norway981.db.html OperonHumanV3.db.html PFAM.db.html POCRCannotation.db.html PartheenMetaData.db.html RaExExonProbesetLocation.html RmiR.Hs.miRNA.html RmiR.hsa.html Roberts2005Annotation.db.html SHDZ.db.html SNPlocs.Hsapiens.dbSNP.20071016.html SNPlocs.Hsapiens.dbSNP.20080617.html SNPlocs.Hsapiens.dbSNP.20090506.html…

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Extract geneID following GO enrichment analysis

Hello, I have performed GO analysis using enrichGO function provided from Clusterprofiler package used in R. This is my code I used for that as follows: ego = enrichGO(gene = df$REFSEQ, OrgDb = “org.At.tair.db”, keyType = “TAIR”, ont = “ALL”, pAdjustMethod = “BH”, pvalueCutoff = 0.05, qvalueCutoff = 0.05, readable…

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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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How to plot the result of compareCluster using ggplot

Hello, I am trying to plot the result of compareCluster. ck = compareCluster(geneCluster = data, fun = enrichGO, OrgDb = “org.At.tair.db”, keyType = “TAIR”, ont = “BP”, pAdjustMethod = “BH”, pvalueCutoff = 0.05, qvalueCutoff = 0.05, readable = TRUE) After this code, I get the result, but there is another…

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How to extract gene ID corresponding to TAIR (arabidopsis key type)? feat. enrichWP

How to extract gene ID corresponding to TAIR (arabidopsis key type)? feat. enrichWP 0 Hello. I am trying to perform enrichWP function using R. I order : enrichWP(geneList, organism = “Arabidopsis thaliana”), but I got this error message as below: > enrichWP(GO$geneList, organism = “Arabidopsis thaliana”) –> No gene can…

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featureCounts problem in reading Gff

Hi, I am performing RNA-seq analysis on 12 samples. After mapping the reads with Hisat2, I want to count the number of reads using feaureCounts, but I reencountered a problem in reading the gff file downloaded from TAIR. (I also tried downloading it from Ensmbl, but no difference). featureCounts -p…

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Bioconductor – BSgenome

Infrastructure for Biostrings-based genome data packages Bioconductor version: 2.5 Infrastructure shared by all the Biostrings-based genome data packages Author: Herve Pages Maintainer: H. Pages <hpages at fhcrc.org> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“BSgenome”) To cite this package in a publication, start R and enter: citation(“BSgenome”) Documentation…

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Phylogenetic and AlphaFold predicted structure analyses provide insights for A1 aspartic protease family classification in Arabidopsis

Introduction Proteases regulate various biological processes including protein synthesis and maturation, activity modification, degradation and turnover. Depending on their catalytic mechanisms, these proteases are primarily classified into cysteine, metallo-, serine, threonine and aspartic protease family (Beers et al., 2004). The latter protease family is known as acid protease family because they…

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“Error parsing strand (?) from GFF line” happenning in gffread, stringtie and cufflinks

“Error parsing strand (?) from GFF line” happenning in gffread, stringtie and cufflinks 0 Hi! I’m working with various genomic data and while trying to use gffread, stringtie and cufflinks I went through the same error: Error parsing strand (?) from GFF line: NC_037304.1 RefSeq gene 58315 59481 . ?…

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Convert ensembl IDs from dataframe to entrez IDs vector

Convert ensembl IDs from dataframe to entrez IDs vector 0 I want to convert ensembl IDs in to entrez IDs to perform Ontology Analysis. I need to create a vector of ensembl IDs and it does not work. library(ChIPpeakAnno) #to use the function convert2EntrezID library(BSgenome.Athaliana.TAIR.TAIR9) #to get the entrez IDs…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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PolyAllele Detail

Polymorphism: FLAG_344G02 Name    FLAG_344G02 Date last modified    2006-09-11 Aliases    344G02 Tair Accession    Polymorphism:1009991284 Type    insertion    Insertion Type    T-DNA Chromosome   unknown Mutagen    T-DNA insertion Mutation Site    gene Associated Polymorphisms Insertion   Species Variant (attribution)   Length   Polymorphic Sequence   Polymorphism…

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Sequence (annotation) databases in 2021

Forum:Sequence (annotation) databases in 2021 1 Hi everyone, So I know there are several threads on this topic already (or tangentially related to it). For example: But these threads are really old now. Things have probably changed quite significantly in the mean time. So I would like to start a…

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