I have a data.frame containing Ensembl IDs in one column; I would like to find corresponding gene symbols for the values of that column and add them to a new column in my data frame. I used bioMaRt...

I'm trying to run an R script (in particular, I am using the "getLineages" function from the Bioconductor package, Slingshot. I'm wondering why the error "vector memory exhausted (li...

I am trying to install Bioconductor into R, using the code on their website. When I type in the code (see bellow) I get an error message saying that some packages can't be updated, the installation...

I was curious to know if there is any bioinformatics tool out there able to process a multiFASTA file giving me infos like number of sequences, length, nucleotide/aminoacid content, etc. and maybe ...

I have a GRanges object and I would like to extend all ranges eg 1kb on both sides, so each range will become 2kb longer. It is strange but I couldn't manage to do this using the inter-range-method...

I'm getting an issue when I try to install Bioconductor for R. I've searched everywhere for solutions however nothing is really working for me. Please, any advice? The downloaded binary packages a...

The current version of the package I would like to use is failing on bioconductor. Yet, the old version used to work. I am wondering how one can install a specific version of a bioconductor packag...

I have a SQLite database like run.sqlite in my local computer. I am making an R package which contains some code and that runs on this SQLite database. How can I make a R package which contains thi...

Got the errors Error : package ‘stringr’ was installed before R 4.0.0: please re-install it and BiocManager Installation path not writeable, unable to update packages: and further down the road rst...

I am trying to pass on an argument to a function, which is a string but must be evaluated both for it's name (symbol?) and it's value (see example below). So far I am able to use base::get to get t...

I'm using ComplexHeatmap to create a heatmap in R. I have recreated a small heatmap here. I can't figure out from the documentation how to adjust the font size for the text on the x-axis. a = matri...

I am trying to install a package in R, but cannot get around the following error. What is going on? :( I am running Fedora 20, R 3.2 biocLite("monocle") BioC_mirror: http://bioconductor.org ...

I need to install different packages on R. The OS is ubuntu for windows. When I try "BiocManager::install("Biobase") I get the following error: ** R ** data ** inst ** byte-compile and prepare pac...

I am trying some tutorials on bioconductor; but I get error messages, that I would like to search/submit; unfortunately, since R is installed on a system configured in french, R returns me messages...

I am working on an R package (https://github.com/bgbrink/dropClust) and I was testing if it can be installed, since it depends on a number of packages both from CRAN and from Bioconductor. I specif...

I have a Run length encoded vector representing some value at every position on the genome, in order. As a toy example suppose I had just one chromosome of length 10, then I would have a vector loo...

I manage the Depends, suggests and imports of the description file. and finally I submit my package to CRAN. But during installation the package, it only install the packages which are deposited un...

I am using biomaRt in R to query ensembl's hsapiens database of human genes. I am using the function getBM to get all genes' name, start position and stop position, but I cannot find the right attr...

I'm quite new to R and I'm trying to use the ComBat script in the R sva library on a 331 x 89 matrix of gene expression values. My data consists of 5 batches and it's ordered in that way so the fir...

everyone! I'm trying to install Bioconductor package "cummeRbund" and constantly fail. I've tried biocLite("cummeRbund") command with BiocInstaller enabled, install.packages("cummeRbund") and thei...

I would like to plot confidence intervals to a data with NAs, using Gviz package. I modified manual example to expose my problem. First as the manual expose: library(Gviz) ## Loading GRanges obj...

I have a data which contain some NA value in their elements. What I want to do is to perform clustering without removing rows where the NA is present. I understand that gower distance measure in ...

I would like to compare two data sets df1 and df2 in such a way that, the unique characters in df2$ID should be added as a new column in df1 and assign df2$Xp value for each gene, if the coordinate...

How do you find the overlapping coordinates and extract the respective seg.mean values for the overlapping region? data1 Rl pValue chr start end CNA 2 2.594433 6 129740000 129780000 gain 2 3.94...

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 goo...