[ensemblVEP][1] had a great function called [parseCSQToGRanges][2] that you could use to get the consequence information in a nice data.frame, e.g. vcf <- readVcf(tempFile, genome="grc38") …

Hello Everyone, I just need to make sure that we can use GWENA R/Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/GWENA.html) in proteomics. although WGCNA is designed for microarrays and …

Hi! I'm trying to use the enrichGO function in the [clusterProfiler package][1] to get significant GO categories for a list of genes from my fungi …

Hi everyone, This is a naive attempt to start collating for the community some key proteomics bioinformatics pipelines and workflows. I am familiar with the …

I am trying to import a Newick format tree into Cystoscape using vinette in Bioconductor. (https://bioconductor.org/packages/release/bioc/vignettes/RCy3/inst/doc/Phylogenetic-trees.html) This works well until I get to this call …

Our computing infrastructure is scheduled for maintenance in the coming week in Monday 2/12 and Tuesday 2/13 (EST). Pathview Web server (https://pathview.uncc.edu) is likely inaccessible …

Hello I am using [myGene][1] in R for annotation. The available list of [genome assemblies][2] is a bit outdated (dm3 for *Drosophila melanogaster*). For instance, …

Dear experts! I had no problem downloading the following packages when I had version 3.0.7 last weekend, but I upgraded to 3.3.3 now. source("http://bioconductor.org/biocLite.R") biocLite("DESeq2") …

Dear biostars forum, I need help with getting the data I want from agilent microarrays from [GEO database GSE59408][1]. I used the Bioconductor package ["limma"][2] …

<p>I have been exploring the R ontoCAT package from Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/ontoCAT.html), but I noticed that there is no method for getting all of the instances …