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Questions tagged [bioconductor]

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data in the R language.

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development.

Resources:

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there is no package called 'BiocInstaller'

Whenever I try to install a new package I'm getting this error: source("http://bioconductor.org/biocLite.R") Warning in install.packages : package ‘BiocInstaller’ is not available (for R version 3.0.2 RC) Installing package into…
on_the_shores_of_linux_sea
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R how to install a specified version of a bioconductor package?

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 package? Thanks in advance. In my case, the package is…
anilbey
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R package DESCRIPTION - Remotes from Bioconductor should install binary

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 specified the three dependencies from Bioconductor in the…
bgbrink
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Efficiently construct GRanges/IRanges from Rle vector

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 looking…
user1356855
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rpy2: Converting a data.frame to a numpy array

I have a data.frame in R. It contains a lot of data : gene expression levels from many (125) arrays. I'd like the data in Python, due mostly to my incompetence in R and the fact that this was supposed to be a 30 minute job. I would like the…
Mike Dewar
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multiFASTA file processing

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 automatically draw descriptive plots. Also an R…
Federico Giorgi
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OpenBLAS issue with ComBat() function of the R Bioconductor SVA package on Torque cluster

I've a problem with ComBat() function from the SVA package of Bioconductor in R. On my laptop (Latitude 5590 running a Linux Ubuntu 18 operating system), it works well. But if I ran it on a TORQUE cluster, the call to the ComBat() function generates…
DavideChicco.it
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'lib = "/usr/lib/R/library"' is not writable" while installing R Bioconductor package

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 their variations with specified library address. The…
SirOsric
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Show all lines in GenomicRange package output

I am working with GenomicRange R package. I have an input file like this: dvex108056 + 87 206 dvex108056 + 87 226 dvex108056 - 101 240 dvex108056 - 104 240 dvex108056 - 59 188 dvex108056 - 68 197 dvex108056 - 70 208 dvex108056 - 75 211 dvex108056 -…
Cristian Velandia
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GenomicFeatures Package Installation Trouble

Sorry to be back so soon with a simple installation question, but my inability to solve it myself is seriously impairing my productivity. Anyway, I tried installing GenomicFeatures as suggested by the BC website. >…
mstrfrdmx
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In writing an R package, using the flowCore::transform function, can I both use a variable name as text and get the actual value?

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 the actual value, but the assignment in…
FM Kerckhof
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Resolving a 'model empty' error in cross-validation for SVM classification when using the CMA Bioconductor package for R

I am using the Bioconductor package CMA to perform internal, Monte Carlo cross-validation (MCCV) on SVM classifiers in a microarray dataset. CMA internally uses the e1071 R package for the SVM work. The dataset has 387 variables (attributes) for 45…
user594694
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How can I specify a package version for bio conductor package in Travis?

I am trying to use travis for my R package. The check are fine for R 3.4, results are here For R 3.3, Travis is KO because Travis install the package rhdf5 but it's not the correct version. Results are here I have in my description file, the…
Maaehj
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Writing and loading expression sets to and from csv files

In R, one can write a bioconductor ExpressionSet into a csv file using csv.write. For example, using the standard bladderbatch data available as a bioconductor package the following code writes a csv file to the current working…
Adam Kurkiewicz
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Best way to get list of SNPs by gene id?

I have a long data frame of genes and various forms of ids for them (e.g. OMIM, Ensembl, Genatlas). I want to get the list of all SNPs that are associated with each gene. (This is the reverse of this question.) So far, the best solution I have found…
CoderGuy123
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