Questions tagged [rstudio]

Integrated Development Environment (IDE) for the R package

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23 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 ...
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0answers
69 views

fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
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1answer
82 views

Help with performing PCA analysis on data from 3 different datasets of normalized counts data for RNA-seq experiment

So, I have limited knowledge of R but I need to do a PCA analysis of 3 different datasets of gene expression as a result of combined growth or mono-culture growth. The 3 different datasets I performed ...
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0answers
87 views

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: ...
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1answer
181 views

How to select specific lines and specific columns

Please I'm a beginner in using R and I work on database. I have a database that contain lot of columns and lines, like this for example ...
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1answer
51 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...
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1answer
683 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 ...
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2answers
118 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 ...
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1answer
3k 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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2answers
3k 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 ...
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2answers
202 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 ...
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0answers
57 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 ?
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1answer
1k 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: ...
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1answer
6k 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: <...
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0answers
488 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 ...
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1answer
67 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 ...
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1answer
441 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 ...