Tag: GOseq

Course. – Gene Set Enrichment Analysis in R/Bioconductor

News:Course. – Gene Set Enrichment Analysis in R/Bioconductor – ONLINE, 22-25 January 0 Dear all, there are still 5 seats for the next edition of the online course on “Gene Set Enrichment Analysis in R/Bioconductor” taking place from January 22nd to January 25th, 2024. This course will cover popular GSEA…

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Accepted r-bioc-goseq 1.54.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 01 Dec 2023 11:53:07 +0100 Source: r-bioc-goseq Architecture: source Version: 1.54.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-goseq (1.54.0-1) unstable; urgency=medium . * New upstream version * Add d/t/autopkgtest-pkg-r.conf Checksums-Sha1: 9a60c9189f597ab34494ac9006a997cc48bcb38f…

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Bioconductor – rtracklayer

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

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Error in Gviz (actually, rtracklayer)

Error in Gviz (actually, rtracklayer) | IdeogramTrack 0 @25075190 Last seen 7 minutes ago South Korea When I run this code (below) iTrack <- IdeogramTrack(genome = “hg19”, chromosome = “chr2”, name = “”) then I get the error Error: failed to load external entity “http://genome.ucsc.edu/FAQ/FAQreleases” Did someone else encounter this…

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Help with interpreting GO enrichment resutls using goseq – usegalaxy.org support

ding66 October 11, 2023, 6:35pm 1 Hi there! I’m new to RNA-Seq results analysis. By following the tutorial of ” Reference-based RNA-Seq data analysis” (Reference-based RNA-Seq data analysis), I have so far completed mapping, annotation, differential expression analysis. Now the next step that I want to do is gene enrichment…

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KEGG Pathway analysis for non-model organism using goseq

KEGG Pathway analysis for non-model organism using goseq 0 Dear all, I have to perform KEGG Pathway analysis of wheat DEGs (differentially expressed genes). I found goseq in R but wheat is not native organism. For GO term analysis of wheat I first retrieved GO term IDs from biomart and…

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Index of /~psgendb/birchhomedir/public_html/doc/local/pkg/MeV_4_8_0/documentation/manual

Name Last modified Size Description Parent Directory   –   2anova1.jpg 2011-09-09 05:55 121K   4.3.1.jpg 2011-09-09 05:55 117K   4.4.1.jpg 2011-09-09 05:55 63K   4.6.1.jpg 2011-09-09 05:55 38K   4.7.1.jpg 2011-09-09 05:55 56K   4.10.1.jpg 2011-09-09 05:55 63K   4.11.1.jpg 2011-09-09 05:55 112K   4.12.1.jpg 2011-09-09 05:55 55K  …

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Gene Set Enrichment Analysis in R/Bioconductor

News:Course – Gene Set Enrichment Analysis in R/Bioconductor 0 Dear all, registrations are open for the next edition of the online course on “Gene Set Enrichment Analysis in R/Bioconductor” taking place from January 22nd to January 25th, 2024. This course will cover popular GSEA tools, both online-based and R packages,…

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Genome-wide identification of lncRNA & mRNA for T2DM

Department of Biotechnology, College of Science, Taif University, Taif, 21944, Saudi Arabia Correspondence: Sarah Albogami, Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia, Email [email protected] Purpose: According to the World Health Organization, Saudi Arabia ranks seventh worldwide in the number of patients with…

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How to load a galaxy DESeq results table into R so i can continue my workflow there

How to load a galaxy DESeq results table into R so i can continue my workflow there 0 Hello i have a DESeq2 results table wich i generated in Galaxy so i download it to R so i can use clusterProfiler and GOseq to do the functional and domain annotation….

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Ubuntu Manpage: goseq – Identify sequence entries containing GO terms

Provided by: emboss_6.6.0+dfsg-11ubuntu1_amd64 NAME goseq – Identify sequence entries containing GO terms SYNOPSIS goseq -sequence seqall -term string -outfile outfile goseq -help DESCRIPTION goseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the “Edit” command group(s). OPTIONS Input section -sequence…

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Accepted r-bioc-goseq 1.52.0-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Thu, 27 Jul 2023 21:47:46 +0200 Source: r-bioc-goseq Architecture: source Version: 1.52.0-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Andreas Tille <ti…@debian.org> Changes: r-bioc-goseq (1.52.0-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1:…

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Problem with goseq – error

Hello, I’m trying to do GO analysis using goseq but I get this error: < In pcls(G) : initial point very close to some inequality constraints Loading required package: AnnotationDbi Loading required package: stats4 Loading required package: BiocGenerics Loading required package: paral>> as input I had this: To add more…

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Gene Set Comparison Without Expression Data

Gene Set Comparison Without Expression Data 1 I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated with Epidermolysis bullosa shows statistically significant,…

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Differentially expressed genes in breast cancer

Introduction Breast cancer represents the most frequently diagnosed and fatal malignant neoplasm among women worldwide. In 2020, breast cancer accounted for the fifth-highest rate of cancer death.1 Current data indicates that cancer is both a hereditary and epigenetic disease. Many major aspects of tumor biology are controlled by epigenetic modifications,…

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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…

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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…

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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…

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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,…

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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…

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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 =…

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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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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…

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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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