Questions tagged [rstudio]
Integrated Development Environment (IDE) for the R package
15 questions
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AMOVA in Rstudio with haploid data
I have haplotype data from mitochondrial DNA, which is divided into different countries and different cities within the countries. I would like to do an AMOVA (analysis of molecular variance), to see ...
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14
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Running multivariate covariance generalized linear model using mcglm()
i am runnig multivariate covariance generalized linear model for the first time. for getting hands on it firstly i am trying to reproduce the example (6.1) from "Bonat, W. H. (2018). Multiple ...
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65
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Why my FeatureScatter looks so different, and what does that mean?
I' am doing a sc-Seq analysis on a dataset from 10x genomics, using Seurat. I followed the standard workflow and I also did it with the SCTransform workflow. The results are very different when I plot ...
1
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1
answer
169
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fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
...
- 11
1
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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
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1
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140
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Get Dockerfile of a bioconda package
Bioconda packages have associated containers images. E.g. bioconductor-csaw has the image quay.io/biocontainers/bioconductor-csaw...
- 343
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2
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1k
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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 ...
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2
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248
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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 ...
- 2,232
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2
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387
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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
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58
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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
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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
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1
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21k
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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:
<...
- 351
2
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683
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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 ...
- 97
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1
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91
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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
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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 ...
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