Questions tagged [rstudio]
Integrated Development Environment (IDE) for the R package
14
questions
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vote
2
answers
177
views
How to input data and metadata from NCBI for RNA-Seq analysis in R
I am quite new to R programming so I hope my question is a clear one and not too confusing.
So, I have downloaded some .txt and .csv files containing the raw count data (I am supposed to find out ...
- 11
1
vote
1
answer
140
views
fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
...
- 11
1
vote
0
answers
108
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I can't launch FastqCleaner I always get a warning message and the application never starts
I tried to install all the needed and related packages but I still did not know what the problem is, Can anyone please help if anything else I can do??
I always get this over and over:
...
- 11
2
votes
1
answer
96
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...
- 323
1
vote
2
answers
971
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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
2
answers
209
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 ...
- 1,765
0
votes
1
answer
5k
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:
...
- 149
1
vote
2
answers
291
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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 ...
- 35
1
vote
0
answers
57
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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 ?
- 39
0
votes
1
answer
2k
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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：
...
- 39
4
votes
1
answer
13k
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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:
<...
- 319
2
votes
0
answers
580
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 ...
- 87
1
vote
1
answer
71
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 ...
- 21
2
votes
1
answer
586
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 ...
- 1,129