# \#rstudio **URL:** https://help.galaxyproject.org/tag/rstudio/350.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [RStudio Interactive Tool cannot be launched](https://help.galaxyproject.org/t/rstudio-interactive-tool-cannot-be-launched/18304)
**Author:** [@luzihao](https://help.galaxyproject.org/u/luzihao)\ **Replies:** 5\ **Last updated:** [August 24, 2026, 11:15am UTC](https://help.galaxyproject.org/t/rstudio-interactive-tool-cannot-be-launched/18304 "2026-08-24T11:15:11Z")
Hello Galaxy support team, I am trying to use the RStudio Interactive Tool in Galaxy, but I have been unable to open it for approximately one month. When I launch RStudio from the Interactive Tools section, the job sta… --- ## [Bioconductor packages failing to install in Galaxy Europe Interactive R (cannot access repository index)](https://help.galaxyproject.org/t/bioconductor-packages-failing-to-install-in-galaxy-europe-interactive-r-cannot-access-repository-index/18086)
**Author:** [@noor\_ali](https://help.galaxyproject.org/u/noor_ali)\ **Replies:** 1\ **Last updated:** [July 28, 2026, 9:15pm UTC](https://help.galaxyproject.org/t/bioconductor-packages-failing-to-install-in-galaxy-europe-interactive-r-cannot-access-repository-index/18086 "2026-07-28T21:15:01Z")
Hello everyone, I am currently using the Galaxy Europe Interactive R environment for a single-cell RNA-seq analysis workflow, but I am running into a persistent issue when trying to install Bioconductor packages. Probl… --- ## [Custom PCA plot in Deseq2](https://help.galaxyproject.org/t/custom-pca-plot-in-deseq2/7433)
**Author:** [@Edling](https://help.galaxyproject.org/u/Edling)\ **Replies:** 3\ **Last updated:** [April 8, 2026, 12:47am UTC](https://help.galaxyproject.org/t/custom-pca-plot-in-deseq2/7433 "2026-04-08T00:47:28Z")
Is there a way of obtaining the actual data tables used for plotting the PCA, MA etc plots that is part of the output when running DeSeq2? Thanks, Charlotte --- ## [RStudio troubleshooting](https://help.galaxyproject.org/t/rstudio-troubleshooting/17578)
**Author:** [@skyward](https://help.galaxyproject.org/u/skyward)\ **Replies:** 2\ **Last updated:** [March 16, 2026, 6:12pm UTC](https://help.galaxyproject.org/t/rstudio-troubleshooting/17578 "2026-03-16T18:12:26Z")
I am having the same issue as Kwang-woo and David83200. I’m trying to run Galaxy’s RStudio 4.6.0 in a new tab. However, although the Interactive Tools area on the left pane menu indicates that the RStudio job is running,… --- ## [Bam index file not loaded in RStudio](https://help.galaxyproject.org/t/bam-index-file-not-loaded-in-rstudio/16126)
**Author:** [@droslj](https://help.galaxyproject.org/u/droslj)\ **Replies:** 5\ **Last updated:** [August 8, 2025, 5:38pm UTC](https://help.galaxyproject.org/t/bam-index-file-not-loaded-in-rstudio/16126 "2025-08-08T17:38:28Z")
When starting RStudio interactive tool and selecting bam files as inputs, bam index files are not loaded into RStudio --- ## [Goseq Overlapping names of GO terms](https://help.galaxyproject.org/t/goseq-overlapping-names-of-go-terms/15802)
**Author:** [@Seraph](https://help.galaxyproject.org/u/Seraph)\ **Replies:** 1\ **Last updated:** [August 5, 2025, 12:59am UTC](https://help.galaxyproject.org/t/goseq-overlapping-names-of-go-terms/15802 "2025-08-05T00:59:39Z")
Dear all, When using GOseq on the Galaxy platform, the resulting dot plot placed two distinct GO terms on the same row because they shared a similar beginning in their descriptions. Specifically, these terms were: GO:0… --- ## [Error on RStudio of the code "read.tree"](https://help.galaxyproject.org/t/error-on-rstudio-of-the-code-read-tree/14530)
**Author:** [@Jane](https://help.galaxyproject.org/u/Jane)\ **Replies:** 1\ **Last updated:** [February 15, 2025, 5:00pm UTC](https://help.galaxyproject.org/t/error-on-rstudio-of-the-code-read-tree/14530 "2025-02-15T17:00:47Z")
Hi everyone, I import a RAxML tree file into the RStudio in the Galaxy. When I used the code: \`\`\` tree ← read.tree(treefile) An error reported as: Warning message: In read.tree(treefile) : no semicolon(s) \[end(s) of… --- ## [Error report on dataset import from Galaxy history into Rstudio](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470)
**Author:** [@Jane](https://help.galaxyproject.org/u/Jane)\ **Replies:** 5\ **Last updated:** [January 20, 2025, 9:12am UTC](https://help.galaxyproject.org/t/error-report-on-dataset-import-from-galaxy-history-into-rstudio/14470 "2025-01-20T09:12:15Z")
Hello everyone, I am trying to import some tsv files from my galaxy history into the Rstudio in usegalaxy.eu. I am continuously getting an error message. The command is: Get the SNP distance matrix object from Galaxy … --- ## [An error reported on Rstudio, bash: syntax error near unexpected token \`('](https://help.galaxyproject.org/t/an-error-reported-on-rstudio-bash-syntax-error-near-unexpected-token/14466)
**Author:** [@Jane](https://help.galaxyproject.org/u/Jane)\ **Replies:** 2\ **Last updated:** [January 16, 2025, 8:20pm UTC](https://help.galaxyproject.org/t/an-error-reported-on-rstudio-bash-syntax-error-near-unexpected-token/14466 "2025-01-16T20:20:01Z")
Dear, I am learning how to Identify transmission clusters in the this Tutorial"https://training.galaxyproject.org/training-material/topics/evolution/tutorials/mtb\_transmission/tutorial.html#identifying-tuberculosis-tran… --- ## [Rstudio startup problem](https://help.galaxyproject.org/t/rstudio-startup-problem/12272)
**Author:** [@vidya\_sagar](https://help.galaxyproject.org/u/vidya_sagar)\ **Replies:** 2\ **Last updated:** [April 24, 2024, 7:15am UTC](https://help.galaxyproject.org/t/rstudio-startup-problem/12272 "2024-04-24T07:15:24Z")
I wanted to follow the following tutorial: Variant Calling Workflow so I tried opening RStudio, by clicking run tool, and the history shows the following: RStudio Add Tags This job is waiting to run. format ipynb, d… --- ## [Error with Rstudio - crashed and impossible to run again](https://help.galaxyproject.org/t/error-with-rstudio-crashed-and-impossible-to-run-again/12219)
**Author:** [@maschwab](https://help.galaxyproject.org/u/maschwab)\ **Replies:** 1\ **Last updated:** [April 23, 2024, 7:58pm UTC](https://help.galaxyproject.org/t/error-with-rstudio-crashed-and-impossible-to-run-again/12219 "2024-04-23T19:58:47Z")
I was running some analyses in Rstudio on the EU server and when i wanted to check if it was finished I got the following error on the webpage : ERR\_TOO\_MANY\_REDIRECTS Since then the job as turned green in my history an… --- ## [Cannot upload seurat object in RStudio](https://help.galaxyproject.org/t/cannot-upload-seurat-object-in-rstudio/11801)
**Author:** [@n\_terway](https://help.galaxyproject.org/u/n_terway)\ **Replies:** 1\ **Last updated:** [February 28, 2024, 10:13am UTC](https://help.galaxyproject.org/t/cannot-upload-seurat-object-in-rstudio/11801 "2024-02-28T10:13:12Z")
Hello! I am trying to upload a Seurat object to RStudio which I am running on Galaxy. The object is ~2.2GB. When I try to upload it in RStudio I get an error message saying “Unexpected response from server”. I suspected… --- ## [Can't upload data with gx\_get() in Rstudio tool or install GalaxyConnect into desktop R Studio](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618)
**Author:** [@sfer3175](https://help.galaxyproject.org/u/sfer3175)\ **Replies:** 5\ **Last updated:** [February 23, 2024, 5:47pm UTC](https://help.galaxyproject.org/t/cant-upload-data-with-gx-get-in-rstudio-tool-or-install-galaxyconnect-into-desktop-r-studio/11618 "2024-02-23T17:47:16Z")
Hello, I’m trying to follow this tutorial that uses gx\_get() to upload datafiles from my history (Galaxy) into the RStudio interactive tool. I’ve created multiple histories and restarted the Rstudio tool multiple times … --- ## [Co-expression analysis, unable to install WGCNA in Rstudio](https://help.galaxyproject.org/t/co-expression-analysis-unable-to-install-wgcna-in-rstudio/11562)
**Author:** [@ro22macha](https://help.galaxyproject.org/u/ro22macha)\ **Replies:** 1\ **Last updated:** [January 23, 2024, 3:08pm UTC](https://help.galaxyproject.org/t/co-expression-analysis-unable-to-install-wgcna-in-rstudio/11562 "2024-01-23T15:08:35Z")
Hi everyone, I’m trying to install WGCNA in Rstudio using the Galaxy platform, but I’m having trouble. I tried using BiocManager::install(“WGCNA”), but I get a warning that the dependency “impute” is not installed. I n… --- ## [Rstudio on Galaxy.eu : installing new packages](https://help.galaxyproject.org/t/rstudio-on-galaxy-eu-installing-new-packages/7000)
**Author:** [@Danielle\_Ireland](https://help.galaxyproject.org/u/Danielle_Ireland)\ **Replies:** 5\ **Last updated:** [July 6, 2023, 11:59pm UTC](https://help.galaxyproject.org/t/rstudio-on-galaxy-eu-installing-new-packages/7000 "2023-07-06T23:59:41Z")
Hello, I’m having trouble installing packages to RStudio on galaxy.eu. I would like to install SNPRelate and its dependent package gdsfmt. I tried following the instructions in RStudio to use conda install : conda ins… --- ## [Jupyter Notebook not available in Active Interactive Tools](https://help.galaxyproject.org/t/jupyter-notebook-not-available-in-active-interactive-tools/10357)
**Author:** [@Kashish\_Kumar](https://help.galaxyproject.org/u/Kashish_Kumar)\ **Replies:** 1\ **Last updated:** [July 6, 2023, 11:56pm UTC](https://help.galaxyproject.org/t/jupyter-notebook-not-available-in-active-interactive-tools/10357 "2023-07-06T23:56:12Z")
Although the instance is running, it shows you do not have active interactive tools yet. I have re-tried launching the tool as well. --- ## [The problem of calling tools](https://help.galaxyproject.org/t/the-problem-of-calling-tools/10274)
**Author:** [@maryam-gh99](https://help.galaxyproject.org/u/maryam-gh99)\ **Replies:** 2\ **Last updated:** [June 19, 2023, 2:42pm UTC](https://help.galaxyproject.org/t/the-problem-of-calling-tools/10274 "2023-06-19T14:42:50Z")
Hello I have two tools “RStudio” and “Interactive JupyTool and notebook” in my history, but when I want to call them from the Active Interactive Tools section,I face with the message you do not have active interactive t… --- ## [How to do differential expression analysis on ATAC-SEQ](https://help.galaxyproject.org/t/how-to-do-differential-expression-analysis-on-atac-seq/10250)
**Author:** [@mfaleevs](https://help.galaxyproject.org/u/mfaleevs)\ **Replies:** 1\ **Last updated:** [June 14, 2023, 7:31pm UTC](https://help.galaxyproject.org/t/how-to-do-differential-expression-analysis-on-atac-seq/10250 "2023-06-14T19:31:41Z")
Hello! My apologies if a stupid question- I have just completed the tutorial on atac-seq analysis for peak calling. I was wondering whether there are any tutorials on how to conduct differential expression between two at… --- ## [Interactive Rstudio Installing new packages](https://help.galaxyproject.org/t/interactive-rstudio-installing-new-packages/9344)
**Author:** [@helenwsung](https://help.galaxyproject.org/u/helenwsung)\ **Replies:** 1\ **Last updated:** [January 24, 2023, 10:23pm UTC](https://help.galaxyproject.org/t/interactive-rstudio-installing-new-packages/9344 "2023-01-24T22:23:26Z")
Hi i’m a bit confused on how to install r packages in the interactive session for Rstudio? If I use the install.packages() in the console, I just get this error: x86\_64-conda-linux-gnu-cc -I"/opt/miniconda/lib/R/includ… --- ## [Cannot install r packages in the interactive session](https://help.galaxyproject.org/t/cannot-install-r-packages-in-the-interactive-session/9228)
**Author:** [@chiwwong](https://help.galaxyproject.org/u/chiwwong)\ **Replies:** 0\ **Last updated:** [December 28, 2022, 8:12am UTC](https://help.galaxyproject.org/t/cannot-install-r-packages-in-the-interactive-session/9228 "2022-12-28T08:12:25Z")
I am working on usegalaxy.eu. I am trying to install the R package dnapath. However, it was halted by the error: /bin/sh: 1: x86\_64-conda-linux-gnu-cc: not found make: \*\*\* \[/opt/miniconda/lib/R/etc/Makeconf:170: C\_FOR… --- ## [Error\_data import from Galaxy history into rstudio](https://help.galaxyproject.org/t/error-data-import-from-galaxy-history-into-rstudio/8730)
**Author:** [@srinivasa\_abishek](https://help.galaxyproject.org/u/srinivasa_abishek)\ **Replies:** 3\ **Last updated:** [October 13, 2022, 8:57pm UTC](https://help.galaxyproject.org/t/error-data-import-from-galaxy-history-into-rstudio/8730 "2022-10-13T20:57:52Z")
Hello there, I am trying to import some txt files from my galaxy history into the Rstudio in usegalaxy.eu. I am continuously getting an error message. first half of the error message: DEBUG:root:Host IP determined to … --- ## [Is there anything available to replace the deprecated Genome Diversity tools](https://help.galaxyproject.org/t/is-there-anything-available-to-replace-the-deprecated-genome-diversity-tools/6953)
**Author:** [@Danielle\_Ireland](https://help.galaxyproject.org/u/Danielle_Ireland)\ **Replies:** 4\ **Last updated:** [November 3, 2021, 3:35pm UTC](https://help.galaxyproject.org/t/is-there-anything-available-to-replace-the-deprecated-genome-diversity-tools/6953 "2021-11-03T15:35:51Z")
Hello, I have generated a VCF detailing the SNPs in 18 individuals from a population. In a pilot study, I had previously used some of the Genome Diversity tools to generate the genotypes for the samples and then visuali… --- ## [The Rstudio on Galaxy: I cannot install the Seurat package](https://help.galaxyproject.org/t/the-rstudio-on-galaxy-i-cannot-install-the-seurat-package/6364)
**Author:** [@Midsummer](https://help.galaxyproject.org/u/Midsummer)\ **Replies:** 12\ **Last updated:** [July 26, 2021, 2:43pm UTC](https://help.galaxyproject.org/t/the-rstudio-on-galaxy-i-cannot-install-the-seurat-package/6364 "2021-07-26T14:43:45Z")
I want to use the Rstudio function on Galaxy. However, I cannot install the Seurat package which I will use for many tasks (it cannot run just by the seurat tool) . I find it may cause by the “png” package which need th… --- ## [Error when importing dataset to Rstudio](https://help.galaxyproject.org/t/error-when-importing-dataset-to-rstudio/6224)
**Author:** [@feanor1914](https://help.galaxyproject.org/u/feanor1914)\ **Replies:** 4\ **Last updated:** [June 18, 2021, 7:18pm UTC](https://help.galaxyproject.org/t/error-when-importing-dataset-to-rstudio/6224 "2021-06-18T19:18:27Z")
Hi everyone, when trying to import a dataset (large .csv file) from my active galaxy history to Rstudio with gx\_get(19056) I get the following error: DEBUG:root:Host IP determined to be b’172.17.0.1\\n’ DEBUG:root:Test…