bioconductor

问题 This question already has answers here : How should I deal with “package 'xxx' is not available (for R version x.y.z)” warning? (15 answers) Closed 5 years ago . I got this when I am trying to install package from bioconductor, but it seems it does not work properly. The manual of this package is here: http://www.bioconductor.org/packages/devel/bioc/manuals/RTN/man/RTN.pdf The package name is RTN. biocLite("RTN") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12

问题 I've been trying to install DESeq2 to do some analysis for a couple days now. R and biocLite are up to date, and I'm running into permission errors when I try to run biocLite("DESeq2") I receive mostly good messages, but at the end I get: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘XML’ had non-zero exit status 2: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘annotate’ had non-zero exit status 3: In

问题 How can I extract sequences from a FASTA file for each of the intervals defined in a BED file using R? The reference genome used is "Gallus gallus" that can be obtained by: source("http://bioconductor.org/biocLite.R") biocLite("BSgenome.Ggallus.UCSC.galGal4") library(BSgenome.Ggallus.UCSC.galGal4) My data file is a result of gRanges package library("GenomicRanges") > olaps GRanges object with 2141 ranges and 0 metadata columns: seqnames ranges strand <Rle> <IRanges> <Rle> [1] chr14 [ 1665929,

问题 I am trying to run ComBat script on a dataset with 2 batches, but I am getting errors and I do not know how to inspect code since I am an R newbie. I am running ComBat method in this way: # Load sva library(sva) # Read expression values dat = read.table('dataset.xls', header=TRUE, sep='\t') # Read sample information file about batches sif = read.delim('sif.tsv', header=TRUE, sep='\t') # Call ComBat ComBat(dat=dat,batch=sif$Batch, mod=NULL) Anyway my output is: Found 2 batches Found 0

问题 I wanted to install "DESeq2" package in R, but it was missing the xml2-config file. I found somewhere that it can be obtained by installing the libxml2 package, but when I tried it gives error that it's not available for R version 3.4.2. Anyone has idea what to do? 回答1: After running what @amarchin wrote it didn't work instantly but R suggested to install libxml2-dev. So I run: sudo apt-get install libxml2-dev in Terminal. And then in R console I typed the code from @amarchin: devtools:

问题 I would like to match up PDB files from the Protein Databank to canonical AA sequences for the protein as displayed in Cosmic or Uniprot. Specifically, what I need to do is pull from the pdb file, the carbon alpha atoms in the backbone and their xyz positions. I also need to pull their actual order in the proteins sequence. For structure 3GFT (Kras - Uniprot Accession Number P01116), this is easy, I can just take the ResSeq number. However, for some other proteins, I can't figure out how this

问题 I am having issues in installing the samr package in R v3.4 MacOS sierra. I get this warning message: "Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘samr’ Do you want to attempt to install these from sources? y/n: y installing the source package ‘samr’ trying URL 'https://cran.rstudio.com/src/contrib/samr_2.0.tar.gz' Content type 'application/x-gzip' length 36702 bytes (35 KB) ================================================== downloaded 35 KB *

问题 I have gene expression data as number of counts for each probe, something like this: library(data.table) mydata <- fread( "molclass,mol.id,sample1,sample2,sample3 negative, negat1, 0, 1, 2 negative, negat2, 2, 1, 1 negative, negat3, 1, 2, 0 endogen, gene1, 30, 15, 10 endogen, gene2, 60, 30, 20 ") My question here is - what would be the best way to perform background subtraction, i.e. for each sampleN column I need to calculate background (let's say it will be the average of all values from

问题 I had a bioconductor package version 1.2.14, and I've just updated it to version 1.4.2 and unfortunately I get different results. I want to make sure this is because of the package update. Is there a way to revert to the old version, or alternatively to remove the current version and specify installation of the old one? Alternatively, I can see the branches on GitHub and I wonder whether they correspond to the different version from Bioconductor. So, can I install from a GitHub branch release

问题 I can't access many Bioconductor packages in R 3.1.1 and I am quite disappointed with that. How can I downgrade from R 3.1.1 to R 3.0.2 or to some other version? Note that this solution is not good enough for me as I don't have any issues with Bioconductor installation. 回答1: As point by @Deleet, this is FOR WINDOWS ONLY . For the rest of the platforms, see: https://support.rstudio.com/hc/en-us/articles/200486138-Changing-R-versions-for-RStudio-desktop Go to: Tools > Global Options > press the