Questions tagged [rstudio]
The rstudio tag has no usage guidance.
10
questions
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2answers
41 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
171 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:
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1
vote
2answers
125 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
18 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
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0answers
37 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
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1answer
467 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
919 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
158 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
59 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
180 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 ...
