Tag: GOseq
Is there a way to get the name or IDs of genes with the goseq table?
Yes please refer to this post: support.bioconductor.org/p/102273/ For my own case, I modified the function # Get the gene lists of “numDFinCat” in GO.wall report getGeneLists <- function(pwf, goterms, genome, ids){ gene2cat <- getgo(rownames(pwf), genome, ids) cat2gene <- split(rep(names(gene2cat), sapply(gene2cat, length)), unlist(gene2cat, use.names = FALSE)) out <- list() for(term in…
Can we use Entrez IDs for GOSeq?
Hi, I have a microarray data that I would like to do GO analysis using GOSeq. However, I have ENTREZ gene ids. When I am trying to convert ENTREZ ids to ENSEMBL ids, I lose several of my genes from the universe, either because of 1:many mappings or no ENSEMBL…
Microbially produced vitamin B12 contributes to the lipid-lowering effect of silymarin
Animals As female mice/rats resist to HFD-induced obesity and NAFLD, male mice/rats were used to induce obesity and NAFLD model by HFD50. Male Wistar (~180 g body weight; 8 weeks old) rats were purchased from Shandong Laboratory Animal Center with the permission number of SCXK 2014–0007 and raised under thermoneutral housing…
Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks | Parasites & Vectors
Benelli G, Wilke A, Beier JC. Aedes albopictus (Asian Tiger Mosquito). Trends Parasitol. 2020;36:942–3. Article Google Scholar Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. Article CAS Google Scholar Bonizzoni M, Gasperi G, Chen X,…
query regarding error in installation of “goseq” R bioconductor package
query regarding error in installation of “goseq” R bioconductor package 0 @6d5973d2 Last seen 19 hours ago India I am trying to install “goseq” Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are…
Wallenius Vs Fisher’s Noncentral Hypergeometric Distribution
I’ve found myself in the situation where goseq fails with some relatively extreme numbers (derived from ChIP-Seq data with extreme changes in the IP target) and have tracked it down to the calls to pWNCHypergeo() library(BiasedUrn) pWNCHypergeo(x = 643, m1 = 643, m2 = 16976, n = 17611, odds =…
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…
A command line tool to generate sequence diagrams
A small command line utility used to generate UML sequence diagrams from a text-base definition file. Inspired by js-sequence-diagram and websequencediagram. Install To install it: go get github.com/lmika/goseq To allow automatic generation of PNG files, build with the im tag (ImageMagick is required): go get -tags im github.com/lmika/goseq Usage goseq…
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…
