Questions tagged [rstudio]
Integrated Development Environment (IDE) for the R package
12
questions
1
vote
1answer
38 views
Get Dockerfile of a bioconda package
Bioconda packages have associated containers images. E.g. bioconductor-csaw has the image quay.io/biocontainers/bioconductor-csaw...
1
vote
1answer
397 views
Why is library(Seurat) causing my R session to have a fatal error?
I recently tried to load library(Seurat) after installing Seurat package. It caused my R studio to have a fatal error and abort my session. I have successfully downloaded it before. I have uninstalled ...
0
votes
2answers
76 views
Uploading files from local computer or web in rstudio cloud
I am using RStudio Cloud for running velocyto R package. So I have tried to import velocyto file from http://pklab.med.harvard.edu/velocyto/mouseBM/SCG71.loom
I tried to upload that like so
But ...
0
votes
1answer
1k views
Seurat VlnPlot presenting expression of multiple genes in a single cluster
Seurat VlnPlots are most commonly used to visualize differences in any given gene expression across multiple clusters or cell types. For example:
...
1
vote
2answers
883 views
Trim Seurat object to contain expression info only for selected genes
I'm working with some large Seurat objects (MOCA, MCA, Tabula Muris) studying gene coexpression, and I'm running into memory issues.
Is it possible to remove all genes in a Seurat object that are ...
1
vote
2answers
68 views
How can I find all the columns available in UniProt.ws package for R?
I am trying to find the subcellular localization of my 10,000 proteins using UniProt.ws package for R. However, I am unable to find all the columns available for query.
I used another package named ...
1
vote
0answers
50 views
failed to install hdf5r [duplicate]
I failed to install hdf5r using this command provided by https://satijalab.org/seurat/mca_loom.html: devtools::install_github(repo = 'hhoeflin/hdf5r'),below is the code,can you help me ?
0
votes
1answer
744 views
R studio failed to install the latest development version of hdf5r from Github (win10)
I install hdf5r following https://github.com/hhoeflin/hdf5r， it shows two methods:
When I use the second method to install from github,it showed many errors：
...
2
votes
1answer
2k views
Error in as.vector(x) : no method for coercing this S4 class to a vector
I tried to run the following code in R studio. Everything worked fine, except at the last step [write.table(mdat, "recount_mdat.csv")] when I tried to export the 'mdat', I got the following error:
<...
2
votes
0answers
295 views
R package CMD check errors
I have written some codes in R for my personal use. The package successfully installed on my personal laptop (where I have written those commands) and working correctly. But when I distributed it to ...
1
vote
1answer
62 views
Creating a computational table to show the number of available genes between all possible pairs of combinations in eight gene lists
I am looking to create a table (on RStudio) that will show the overlap between 8 different gene lists wherever possible. I have saved the 8 lists as .txt files all in one folder and set that ...
2
votes
1answer
277 views
ScaleData() from Seurat causes crash on RStudio Cloud
Using the sample data in the 2,700 PBMC clustering tutorial, the session crashes at the ScaleData() step. The progress bar remains at 0% and hangs, followed by an R ...
