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6 votes
Accepted

Error in as.vector(x) : no method for coercing this S4 class to a vector

You can't cbind a bunch of obscure object types. If you want merged count tables you should do this: mdat <- do.call(cbind,lapply(dat,assay)) Where row.names ...
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  • 1,498
2 votes

R studio failed to install the latest development version of hdf5r from Github (win10)

Try running this: source("https://bioconductor.org/biocLite.R") biocLite("hdf5r") Just a different method of installing packages besides github. It is more ...
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  • 796
2 votes
Accepted

ScaleData() from Seurat causes crash on RStudio Cloud

It seems RStudio server doesn't know it's limitations. Currently, Projects are limited to 1GB of RAM. Using the R package ulimit which mirrors the function of ...
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  • 1,119
2 votes
Accepted

Seurat VlnPlot presenting expression of multiple genes in a single cluster

To do so one workaround it to have your data in "long format" and then use the column that holds the "gene names" as the x variable while plotting. You can use <...
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  • 3,477
2 votes

Trim Seurat object to contain expression info only for selected genes

A different approach if you are using Seurat3, is DietSeurat(). It allows you to diet the object by removing the components that ...
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  • 507
2 votes

fastqCleaner failing to launch in RStudio

The issue is with the navbar page, downgrading shiny to 1.6 or in my case 1.4 fixed it for me, the detailed link to find to the solution is here: https://github.com/rstudio/shiny/issues/3556 Cheers.
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1 vote

How to input data and metadata from NCBI for RNA-Seq analysis in R

I don't expect the soft or matrix files will be useful for you, although it might be possible to pull metadata out of those files if absolutely necessary. I usually only see those for microarray data, ...
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  • 11.8k
1 vote

How to input data and metadata from NCBI for RNA-Seq analysis in R

A metadata file isn't that large or complicated. If you want to do DE, you must have two treatments? Or two timepoints? Two or more something, and you are comparing samples of one type to another? ...
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  • 1,672
1 vote

How to select specific lines and specific columns

You can simply use subset function in R and use the code given below, ...
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1 vote
Accepted

Get Dockerfile of a bioconda package

The Dockerfile is generated by galaxy-utils, so I'm not entirely sure what it looks like. However you should be able to generate such a "mulled" container as documented here. In short, ...
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  • 19.2k
1 vote

Why is library(Seurat) causing my R session to have a fatal error?

If you haven't already done so I would make a complete installation of Anaconda, particularly good with bash. The I would either install using Anaconda Navigator, or ... ...
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  • 7,721
1 vote

Uploading files from local computer or web in rstudio cloud

Velocyto.R I'm not sure that your issues is from RStudio cloud but more about how you are trying to open the file. The file that you are trying to import is not a ...
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  • 1,011
1 vote

Uploading files from local computer or web in rstudio cloud

This seems to be an encoding problem (certain characters not being recognized), see this, this and also this. Probably the file "/cloud/project/SCG71.loom" is ...
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  • 3,477
1 vote
Accepted

Trim Seurat object to contain expression info only for selected genes

Is your memory usage low enough that you can initially read everything in and then filter later? If so you could read the Seurat object in like normal and then use ...
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  • 429
1 vote
Accepted

How can I find all the columns available in UniProt.ws package for R?

From the UniProt.ws manual: columns shows which kinds of data can be returned for the ...
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  • 3,477
1 vote

How can I find all the columns available in UniProt.ws package for R?

Do you have a small sample of the proteins you are looking for and what you have tried so far in R using Uniprot.ws ? (including output of it), it could be helpful to identify your problem and how to ...
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  • 1,011
1 vote

Creating a computational table to show the number of available genes between all possible pairs of combinations in eight gene lists

To make a confusion matrix of 4 lists against 4 other lists, you need to get the length of all intersecting genes for each pair. Here an example with letters instead of gene names. ...
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  • 3,551

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