[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") …

Hi everyone, I want to perform genie3 for GSE71729 with Bioconductor: https://bioconductor.org/packages/release/bioc/html/GENIE3.html after getting the results from weightMat <- GENIE3(exprMatr), I have no idea what …

Hello Anybody could you please let me know 1) Which one is most suitable package for Isoform quantification 2) What should be the form of …

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 …

Hi, I am analyzing some samples that were analyzed for methylation sites on an EPIC Methylation array (https://emea.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html). I am trying to analyze it using …

Dear all, referring to the batch correction methods for scRNA-seq, would you have any preference and/or comments ? among possible choices : -- MNNCorrect, as …

Does anyone have experience with the [massiR package](https://bioconductor.org/packages/release/bioc/html/massiR.html) in R? I have the following script: probes <- data.frame(y.probes["affy_hg_u133_plus_2"]) massi.y.out <- massi_y(set8, probes) massi_y_plot(massi.y.out) Error in …

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 …

I have a custom CDF and I'd like to create a .db package like [this one](https://bioconductor.org/packages/release/data/annotation/html/hgu133plus2.db.html). Does anyone know what package I can use to …

I am interested in Bioconductor and I want to dive into their stats pages. - [Index of the most used Bioconductor software packages][1] - [The …