Tag: topGO

DOI: 10.18129/B9.bioc.hgu95av2.db   Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) Bioconductor version: Release (3.18) Affymetrix Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories Author: Marc Carlson Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“hgu95av2.db”)): Installation To install this package,…

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

Gene Ontology enrichment with BINGO and ClueGO 0 Hi, I would like to run some GO BP enrichment analysis in Cytoscape (not GSEA based on expression or rankings, just hypergeometric tests on shortlist vs. reference). There are two conditions I would like to fulfill when carrying it out: 1-To be…

Aguilera F, McDougall C, Degnan BM (2017) Co-option and de novo gene evolution underlie molluscan shell diversity. Mol Biol Evol 34(4):779–792 CAS  PubMed  PubMed Central  Google Scholar  Alexa A, Rahnenfuhrer J (2020) topGO: Enrichment analysis for gene ontology. R package version 2.40.0 Google Scholar  Arivalagan J, Yarra T, Marie B,…

Claussnitzer, M. et al. A brief history of human disease genetics. Nature 577, 179–189 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190–1195 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Gusev, A. et…

Hi, I am encountering a strange occurrence with topGO and I don’t understand some of the output I am getting. Using the following relatively straight forward code myGOdata <- new(“topGOdata”, description=”My project”, ontology=”BP”, allGenes=geneList, annot = annFUN.gene2GO, gene2GO = geneID2GO) resultFisherweight <- runTest(myGOdata, algorithm=”weight01″, statistic=”fisher”) resultFisherclassic <- runTest(myGOdata, algorithm=”classic”, statistic=”fisher”)…

Keratinocyte and fibroblast cultures Normal human skin was obtained from surgical residues of breast reduction surgery, with the patients’ written informed consent in accordance with the Helsinki Declaration and with Article L. 1243-4 of the French Code of Public Health. Patients’ written informed consents were collected and kept by the…

DOI: 10.18129/B9.bioc.cellTree     This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see cellTree. Inference and visualisation of Single-Cell RNA-seq data as a hierarchical tree structure Bioconductor version: 3.14 This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell RNA-seq data and builds…

Baumgartner, K., Coetzee, M. P. A. & Hoffmeister, D. Secrets of the subterranean pathosystem of Armillaria: subterranean pathosystem of Armillaria. Mol. Plant Pathol. 12, 515–534 (2011). Article  PubMed  PubMed Central  Google Scholar  Heinzelmann, R. et al. Latest advances and future perspectives in Armillaria research. Can. J. Plant. Pathol. 41, 1–23…

How ti identify genes per terms in with topGO for scRNAseq dataset 0 Hi all, I want to to perform Gene Ontology (GO) Enrichment of Genes Expressed in specific clusters and I am following this tutorial but in the output I cannot find which genes are associated per terms. How…

Genetic targeting of CCK+ interneurons restricted by the Dlx5/6 driver line in mouse hippocampus and neocortex CCK isoforms and their preprohormone can be expressed in excitatory neurons in addition to GABAergic interneurons [28]. In order to target CCK+ inhibitory interneurons only, we employed an intersectional genetic strategy by simultaneous co-expression…

DOI: 10.18129/B9.bioc.APL     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see APL. Association Plots Bioconductor version: 3.15 APL is a package developed for computation of Association Plots (AP), a method for visualization and analysis of single cell transcriptomics data. The main focus…

Avise J (2008) Clonality: the genetics, ecology, and evolution of sexual abstinence in vertebrate animals. Oxford University Press, USA Book  Google Scholar  Avise JC (2015) Evolutionary perspectives on clonal reproduction in vertebrate animals. Proc Natl Acad Sci USA 112(29):8867–8873 Article  CAS  PubMed  PubMed Central  Google Scholar  Andrews S (2010) FastQC:…

Visualization App for RNASeq Differential Expression and Enrichment Analysis 0 Hello, I am looking to see what the latest and greatest is in terms of an app to visualize the results of a differential expression analysis of an RNASeq dataset, including any subsequent enrichment analyses. Ideally this app would take…

2 hours ago Neel &utrif; 20 Hi, I have read this paper www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000309#tab2, where author had done pangenome and their functional annotation. Now i am unable to figure out how did they perform functional enrichment analysis, i.e. the input file for topGO analysis how did they prepared. sorry for silly…

topGO – duplicate genes 0 I am using topGO for phosphoproteomic data, however, since the data is phosphorylated, we have the same proteins and genes. I am now dealing with duplicate gene names for this, how does topGO deal with duplicate gene names and how do I go about this…

This is my code : library(topGO) hs_topGOdata <- new(“topGOdata”, description = “Human proteins”, ontology = c(“BP”), allGenes = allGenes.hs, geneSel = interestingpValues.hs, nodeSize=5, annot = annFUN.gene2GO, gene2GO = geneID2GO.hs) resultFisher <- runTest(hs_topGOdata, algorithm = “classic”, statistic = “fisher”) resultFisher resultFisher.elim <- runTest(hs_topGOdata, algorithm = “elim”, statistic = “fisher”) resultFisher.elim resultKS…

How to make “Custom annotation File” for GO analysis using TOPgo 0 Hello Biostars, I would like to perform GO analysis using R package called Topgo. I have deseq data as well as GO term ID gained after functional annotation as image present here. Using these information, I would like…

KEGG enrichment in R and gene IDs 2 @239caad3 Last seen 3 days ago Belgium Hi, I am trying to run a KEGG enrichment analysis on my data. My genes are in SYMBOL, which I converted to ENTREZID, but I need them in “kegg” or “ncbi-geneID” to run enrichKEGG. I…

DOI: 10.18129/B9.bioc.Rgraphviz     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Rgraphviz. Provides plotting capabilities for R graph objects Bioconductor version: 3.13 Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package. Author: Kasper…

mapping GO terms to classifications one rank down from the top- level GO categories 1 Hi all! I would like to map a list of GO terms (>1000, won’t be able to do it manually) from different GO ranks to one classifications one rank down from the top- level GO…

Mapping GO terms to description and vice versa 1 Hi all! I have a list of GO terms and I would like to find the description of them. Is there a software or package that I can use? Also, how can I find the GO terms based on its description?…

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…

Vamosi, J. C., Magallon, S., Mayrose, I., Otto, S. P. & Sauquet, H. Macroevolutionary patterns of flowering plant speciation and extinction. Annu. Rev. Plant Biol. 69, 685–706 (2018). CAS  PubMed  Google Scholar  Rhymer, J. M. & Simberloff, D. Extinction by hybridization and introgression. Annu. Rev. Ecol. Syst. 27, 83–109 (1996)….

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…

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

DOI: 10.18129/B9.bioc.Ringo     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Ringo. R Investigation of ChIP-chip Oligoarrays Bioconductor version: 3.9 The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data…

DOI: 10.18129/B9.bioc.FoldGO     Package for Fold-specific GO Terms Recognition Bioconductor version: Release (3.13) FoldGO is a package designed to annotate gene sets derived from expression experiments and identify fold-change-specific GO terms. Author: Daniil Wiebe <daniil.wiebe at gmail.com> [aut, cre] Maintainer: Daniil Wiebe <daniil.wiebe at gmail.com> Citation (from within R,…

Batch conversion of InterPro IDs to GO IDS for TopGO analysis 0 Hi all, I have a list of about two thousand InterPro IDs that I would like to convert to their corresponding GO IDs for subsequent enrichment analyses in TopGO. I initially used the Interpro2go batch text file to…