Categories
Tag: GOSemSim
Bioconductor – clusterProfiler
DOI: 10.18129/B9.bioc.clusterProfiler This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see clusterProfiler. statistical analysis and visualization of functional profiles for genes and gene clusters Bioconductor version: 3.12 This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene…
removeBatchEffect with non-linear model fit
removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…
Bioconductor – GOSemSim
This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GOSemSim. GO-terms Semantic Similarity Measures Bioconductor version: 3.2 Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for estimating GO semantic similarities. Support many species, including Anopheles, Arabidopsis, Bovine, Canine,…
Bioconductor – ReactomePA
This package is for version 2.12 of Bioconductor; for the stable, up-to-date release version, see ReactomePA. Reactome Pathway Analysis Bioconductor version: 2.12 This package provides functions for pathway analysis based on REACTOME pathway database. It will implement enrichment analysis, gene set enrichment analysis and functional modules detection. Author:…
Bioconductor – AnnotationHub
DOI: 10.18129/B9.bioc.AnnotationHub Client to access AnnotationHub resources Bioconductor version: Release (3.6) This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be…
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…
Error creating SPIA data for KEGG Orthology (KO) Database KEGG xml files
Hi all, I’m trying to create a SPIA data file for all 483 xml files for the KEGG Orthology (KO) Database. I’m working with a non-model organism that is not supported by KEGG as it’s own organism, so I have to use the KEGG Orthology (KO) Database instead of a…
DeSeq2 data comparison and extracting outputs
Hi, I have an RNA-seq experiment where there are 2 conditions and 2 genotypes. I am trying to figure out how to output the 2 conditions with 2 genotypes from the dds object. I have read online resources, however, it is still not clear what is extracted. I followed and…
Accepted r-bioc-gosemsim 2.26.1-1 (source) into unstable
—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA256 Format: 1.8 Date: Wed, 26 Jul 2023 22:34:49 +0200 Source: r-bioc-gosemsim Architecture: source Version: 2.26.1-1 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-gosemsim (2.26.1-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.2 (routine-update) *…
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…
difference between mgeneSim and mgoSim
Hi everyone, I’m trying to use GoSemSim but I’m struggling due to his results. I started using mgeneSim function, and i passed an array of 11000+ EntrezID genes. It gave me a similarity matrix with some columns and rows all containing value “1”. I think is because, after mapping the…
Parallel and convergent genomic changes underlie independent subterranean colonization across beetles
Conway Morris, S. The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften 96, 1313–1337 (2009). Article ADS CAS PubMed Google Scholar Stern, D. L. The genetic causes of convergent evolution. Nat. Rev. Genet. 14, 751–764 (2013). Article CAS PubMed Google Scholar Christiansen, K. Convergence and parallelism in cave entomobryinae….
Answer: GSEA and GO Ontology
There are a couple of different approaches. 1) you can run similarity and difference metrics on those pathways themselves. for instance, suppose you have three pathways: pathwayA=c(‘A’,’B’,’C’,’D’,’E’,’F’) pathwayB=c(‘A’,’B’,’C’,’D’,’Q’,’F’) pathwayC=c(‘Z’,’Y’,’X’,’W’,’Q’,’J’) pathwayA and B are more similar to each other than pathwayA and pathwayC. You do not need to rely on ontologies…
Establishment of risk model, analysis of immunoinfiltration
Introduction Atrial fibrillation (AF) is a tachyarrhythmia whose incidence and prevalence are steadily increasing with better chronic disease management in the aging global population. As of 2020, 37.5 million patients worldwide were affected by AF, accounting for 0.51% of the global population.1 As a common arrhythmia, AF greatly increases the…
Handling NA’s in Deseq2
Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…
lfcshrink error DESeq2
Hello! I’m having problems with lfcShrink in my DESeq2 workflow. I’m trying to do a differential expression analysis (with only one comparison term: “MULTIseq_ID_call2”) on my single-cell data. However when I do lfcShrink I get an error that I cannot interpret. Can you help me? dds <- DESeq(dds, test =…
Strange Cook’s Values with DESeq2
Hi, I’m currently trying to assess fold change when comparing two different sample types using DESeq2 package and I’m getting weird Cook’s distance values which are causing major problems. The two different samples have different amounts of replicates (6 replicates vs 5 replicates) which might be the reason for these…
function mgeneSim() is resulting in similarity matrix without 1s od diagonal
Hi, How is it possible that in the similarity matrix resulting from the mgeneSim() function (gene semantic similarity measurement, R package GoSemSIm), there are no 1’s on the diagonal ? They are only there when using the measure=”Wang” method but for the rest, such as “Resnik”, “Rel” etc. there is…
Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics
Yu, Z., Loisel, J., Brosseau, D. P., Beilman, D. W. & Hunt, S. J. Global peatland dynamics since the Last Glacial Maximum. Geophys. Res. Lett. 37, L13402 (2010). van Breemen, N. How Sphagnum bogs down other plants. Trends Ecol. Evol. 10, 270–275 (1995). Article Google Scholar Johnson, M. G. et…
Unable to install clusterProfiler on Mac M1
Hi, I failed to install clusterProfiler on Mac M1. May I ask the solution >BiocManager::install(“clusterProfiler”) Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.3 (2022-03-10) Installing package(s) ‘clusterProfiler’ also installing the dependencies ‘fgsea’, ‘DOSE’, ‘enrichplot’, ‘GOSemSim’ Warning: unable to access index for repository bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1: cannot open URL ‘https://bioconductor.org/packages/3.14/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES’ Warning: unable to access…
Error in UseMethod(“rescale”)
Error in UseMethod(“rescale”) 0 @2528ae94 Last seen 17 hours ago United States While using cnetplot to plot enrichGo results, I am getting the following error. It used to work before, but now I am constantly getting this error. I am using clusterprofiler package gse <- enrichGO(gene = deGenes, ont =…
Regarding functional similarity analysis by GOSemSim package of R
Regarding functional similarity analysis by GOSemSim package of R 0 Hi all I am struggling with calculating the functional similarity analysis between two different set of GO terms (list) and a set of negative control. GOSemSim package of R is providing overall score and not individual score (so that t-test…
Bioconductor Forum
James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…