# Help **URL:** https://help.c-moor.org/c/help/7.md [Latest](https://help.c-moor.org/latest.md) · [Categories](https://help.c-moor.org/categories.md) · [Tags](https://help.c-moor.org/tags.md) --- ## [AnVIL Guides and FAQ](https://help.c-moor.org/t/anvil-guides-and-faq/641)
**Author:** [@syork](https://help.c-moor.org/u/syork)\ **Replies:** 0\ **Last updated:** [November 13, 2025, 11:57pm UTC](https://help.c-moor.org/t/anvil-guides-and-faq/641 "2025-11-13T23:57:25Z")
Last updated: November 2025 Guides Access the class workspace Create an RStudio Environment Launch a module Close out a session on AnVIL FAQs I don’t see my class workspace Google synching permissions error The file e… --- ## [SciServer Guides and FAQs](https://help.c-moor.org/t/sciserver-guides-and-faqs/22)
**Author:** [@KatherineCox](https://help.c-moor.org/u/KatherineCox)\ **Replies:** 0\ **Last updated:** [May 13, 2021, 7:09pm UTC](https://help.c-moor.org/t/sciserver-guides-and-faqs/22 "2021-05-13T19:09:56Z")
Guides Start C-MOOR LearnR Container Start C-MOOR RStudio Container FAQs I can’t find a tutorial Start C-MOOR LearnR Container This video (video)(slides) shows you how to create and start up a C-MOOR LearnR compute … --- ## [About the Help category (Start here!)](https://help.c-moor.org/t/about-the-help-category-start-here/17)
**Author:** [@KatherineCox](https://help.c-moor.org/u/KatherineCox)\ **Replies:** 0\ **Last updated:** [April 16, 2021, 7:24pm UTC](https://help.c-moor.org/t/about-the-help-category-start-here/17 "2021-04-16T19:24:34Z")
About the Help category This category is used to ask questions related to technical issues, particularly coding related. While this category is not explicitly limited to coding questions please note the following before … --- ## [Coding Issue - PhyloSeq to Deseq](https://help.c-moor.org/t/coding-issue-phyloseq-to-deseq/876)
**Author:** [@LuisGB](https://help.c-moor.org/u/LuisGB)\ **Replies:** 1\ **Last updated:** [May 18, 2026, 6:42pm UTC](https://help.c-moor.org/t/coding-issue-phyloseq-to-deseq/876 "2026-05-18T18:42:13Z")
Hello, I am trying to use deseq on my analysis of the FeFiFo study data. However, when I run my code I get an error saying “all samples have 0 counts for all genes. check the counting script” Code: Could anyone hel… --- ## [Coding Question - Are there limits on subsets?](https://help.c-moor.org/t/coding-question-are-there-limits-on-subsets/875)
**Author:** [@ksgeorge95](https://help.c-moor.org/u/ksgeorge95)\ **Replies:** 4\ **Last updated:** [May 2, 2026, 2:02am UTC](https://help.c-moor.org/t/coding-question-are-there-limits-on-subsets/875 "2026-05-02T02:02:07Z")
Hi, I’m trying to get the bar plots by subsetting different variables (diet, gender, timepoint, family (Ruminococcaceae) in fefifo study as I’m looking into how has the abundance of this taxa changed over the course of … --- ## [Trouble plotting gene across all regions](https://help.c-moor.org/t/trouble-plotting-gene-across-all-regions/647)
**Author:** [@jenna.nii](https://help.c-moor.org/u/jenna.nii)\ **Replies:** 5\ **Last updated:** [December 3, 2025, 4:10am UTC](https://help.c-moor.org/t/trouble-plotting-gene-across-all-regions/647 "2025-12-03T04:10:18Z")
Does anyone know how I can bypass the “subscript out of bounds” error on the plotting across all regions for the Flybase ID FBgn0283427 (FASN1). We have tried similar and different genes that have worked but this is t… --- ## [R-Coding/Programming Resources/Practice(s) for Beginners](https://help.c-moor.org/t/r-coding-programming-resources-practice-s-for-beginners/586)
**Author:** [@gio](https://help.c-moor.org/u/gio)\ **Replies:** 4\ **Last updated:** [September 16, 2025, 6:01pm UTC](https://help.c-moor.org/t/r-coding-programming-resources-practice-s-for-beginners/586 "2025-09-16T18:01:47Z")
Does anyone know of any helpful and tangible resources/practices/programs for learning how to R-Code? I did locate the following resource(s): Introduction to R for Data Science The goal is to become fluent in R. Thank y… --- ## [Every gene contains at least one zero, cannot compute log geometric means](https://help.c-moor.org/t/every-gene-contains-at-least-one-zero-cannot-compute-log-geometric-means/560)
**Author:** [@syork](https://help.c-moor.org/u/syork)\ **Replies:** 5\ **Last updated:** [July 20, 2025, 7:22pm UTC](https://help.c-moor.org/t/every-gene-contains-at-least-one-zero-cannot-compute-log-geometric-means/560 "2025-07-20T19:22:08Z")
When running differential expression analysis, we see this error: my\_ad\_DESeq2 \<- phyloseq\_to\_deseq2(ad\_counts, design = ~group) my\_comparison \<- c("group", "AD", "control") Significant\_DEseq2\_ASVs \<- Differential\_Abund… --- ## [Trouble with tax plots](https://help.c-moor.org/t/trouble-with-tax-plots/559)
**Author:** [@gugulethusk](https://help.c-moor.org/u/gugulethusk)\ **Replies:** 1\ **Last updated:** [July 17, 2025, 4:25pm UTC](https://help.c-moor.org/t/trouble-with-tax-plots/559 "2025-07-17T16:25:01Z")
I keep getting almost completely black bar plots when subsetting 16s data. Like this: @syork I’ve tried reloading and changing browsers, deleting and creating a new container, to no avail. Is there a problem with… --- ## [Trouble accepting invitation to sciserver](https://help.c-moor.org/t/trouble-accepting-invitation-to-sciserver/259)
**Author:** [@RosaAlcazar](https://help.c-moor.org/u/RosaAlcazar)\ **Replies:** 0\ **Last updated:** [June 7, 2022, 9:39pm UTC](https://help.c-moor.org/t/trouble-accepting-invitation-to-sciserver/259 "2022-06-07T21:39:42Z")
@lulu can you check if you received a new invitation to sciserver.org? I rescinded the previous one and sent another. Also, please go to SciServer User Dashboard and take a screenshot of what you see --- ## [When making website I keep getting an error](https://help.c-moor.org/t/when-making-website-i-keep-getting-an-error/314)
**Author:** [@ShamounDivanyan](https://help.c-moor.org/u/ShamounDivanyan)\ **Replies:** 0\ **Last updated:** [July 22, 2022, 10:56pm UTC](https://help.c-moor.org/t/when-making-website-i-keep-getting-an-error/314 "2022-07-22T22:56:25Z")
I need help with this ASAP because I am going to be out of town for a week soon, with no internet access --- ## [How to use Cutadapt](https://help.c-moor.org/t/how-to-use-cutadapt/487)
**Author:** [@abrahma](https://help.c-moor.org/u/abrahma)\ **Replies:** 1\ **Last updated:** [April 1, 2025, 12:53pm UTC](https://help.c-moor.org/t/how-to-use-cutadapt/487 "2025-04-01T12:53:45Z")
I have a lot of low quality reads on this dataset. How do I use cutadapt to clean up this dataset? --- ## [Need Coding Help](https://help.c-moor.org/t/need-coding-help/466)
**Author:** [@graceekalle](https://help.c-moor.org/u/graceekalle)\ **Replies:** 5\ **Last updated:** [March 6, 2025, 8:29pm UTC](https://help.c-moor.org/t/need-coding-help/466 "2025-03-06T20:29:59Z")
Hi! I am trying to work through a coding tutorial on R on a public restroom bacteria dataset. I’ll link it here: DIY: public restroom bacteria As I am importing my data ( The zipfile has been moved to a new location: h… --- ## [Need help splitting data set for Lamb Gut - SRR10963010 and SRR14289618](https://help.c-moor.org/t/need-help-splitting-data-set-for-lamb-gut-srr10963010-and-srr14289618/464)
**Author:** [@Disomi](https://help.c-moor.org/u/Disomi)\ **Replies:** 1\ **Last updated:** [February 26, 2025, 5:37pm UTC](https://help.c-moor.org/t/need-help-splitting-data-set-for-lamb-gut-srr10963010-and-srr14289618/464 "2025-02-26T17:37:26Z")
I have two large datasets for the lamb gut and could not run taxonomy profiling or genome assembly, so I attempted to split the datasets into chunks they re-run the workflows but galaxy is not allowing me to run “split f… --- ## [Medaka not working on Assemble Genomes Public Workflow on Galaxy](https://help.c-moor.org/t/medaka-not-working-on-assemble-genomes-public-workflow-on-galaxy/447)
**Author:** [@newhe](https://help.c-moor.org/u/newhe)\ **Replies:** 1\ **Last updated:** [February 18, 2025, 7:25pm UTC](https://help.c-moor.org/t/medaka-not-working-on-assemble-genomes-public-workflow-on-galaxy/447 "2025-02-18T19:25:53Z")
Please find attached my history. I was running some samples and none of them were able to load the medaka section of the workflow. AB1 Combined parent sample: Galaxy --- ## [Galaxy Visualization of WGS dataset for C.elegans](https://help.c-moor.org/t/galaxy-visualization-of-wgs-dataset-for-c-elegans/442)
**Author:** [@newhe](https://help.c-moor.org/u/newhe)\ **Replies:** 1\ **Last updated:** [February 12, 2025, 4:40pm UTC](https://help.c-moor.org/t/galaxy-visualization-of-wgs-dataset-for-c-elegans/442 "2025-02-12T16:40:23Z")
Please find attached this link to my galaxy history. I was stuck trying to complete the walkthrough using this dataset. --- ## [readCounts questions for RNA-Seq Mini Cure](https://help.c-moor.org/t/readcounts-questions-for-rna-seq-mini-cure/362)
**Author:** [@Asawa](https://help.c-moor.org/u/Asawa)\ **Replies:** 1\ **Last updated:** [January 16, 2025, 6:14pm UTC](https://help.c-moor.org/t/readcounts-questions-for-rna-seq-mini-cure/362 "2025-01-16T18:14:44Z")
We are using the Marianes mid-gut data to do an RNASeq miniCure. My students are measuring the expression of genes involved in immune pathways along the length of the midgut. Our question has to do with how to normalize … --- ## [How to navigate chapter 7 in miniCURE-BioDIGS](https://help.c-moor.org/t/how-to-navigate-chapter-7-in-minicure-biodigs/356)
**Author:** [@gauriipaul](https://help.c-moor.org/u/gauriipaul)\ **Replies:** 4\ **Last updated:** [January 13, 2025, 1:31am UTC](https://help.c-moor.org/t/how-to-navigate-chapter-7-in-minicure-biodigs/356 "2025-01-13T01:31:42Z")
I was trying the test version of miniCURE for BioDIGS, when I got stuck in Chapter 7 (Kickstart project work). I am having trouble in calculating summary statistics by running the ‘nanoplot’ in Activity 2 – Adjust for Pa… --- ## [Willing to help with Public Dataset!](https://help.c-moor.org/t/willing-to-help-with-public-dataset/353)
**Author:** [@Loraye21](https://help.c-moor.org/u/Loraye21)\ **Replies:** 3\ **Last updated:** [November 26, 2024, 10:08pm UTC](https://help.c-moor.org/t/willing-to-help-with-public-dataset/353 "2024-11-26T22:08:52Z")
Hi! My partner and I are looking for a new project to do, and we are willing to help out with locating public datasets associated with: Human Gut Water Soil If anyone can help thank you in advance! -Loraye Smith an… --- ## [Help! I need to turn this Data set into a krona pie chart](https://help.c-moor.org/t/help-i-need-to-turn-this-data-set-into-a-krona-pie-chart/351)
**Author:** [@ekallegrace](https://help.c-moor.org/u/ekallegrace)\ **Replies:** 3\ **Last updated:** [November 20, 2024, 3:17pm UTC](https://help.c-moor.org/t/help-i-need-to-turn-this-data-set-into-a-krona-pie-chart/351 "2024-11-20T15:17:50Z")
When I try to run my dataset (SRR-it is a very large dataset) into trim QC to trim it, it always stops running at the Fastp job. An error sign shows saying that there isn’t enough memory for the job to run. So i realized… --- ## ["commit changes" button in git wont work](https://help.c-moor.org/t/commit-changes-button-in-git-wont-work/316)
**Author:** [@lulu](https://help.c-moor.org/u/lulu)\ **Replies:** 1\ **Last updated:** [July 26, 2022, 6:51pm UTC](https://help.c-moor.org/t/commit-changes-button-in-git-wont-work/316 "2022-07-26T18:51:25Z")
I can not commit my changes to git but it worked fine when other people committed for me and i just accepted the merge request. I don’t know if it a problem with my account as I am unable to make commits to projects i… --- ## [Please ignore (r4ds submission)](https://help.c-moor.org/t/please-ignore-r4ds-submission/315)
**Author:** [@lulu](https://help.c-moor.org/u/lulu)\ **Replies:** 0\ **Last updated:** [July 24, 2022, 4:21am UTC](https://help.c-moor.org/t/please-ignore-r4ds-submission/315 "2022-07-24T04:21:02Z")
--- ## [Unable to get any data Wnt1 or Wnt10b in R-Studio](https://help.c-moor.org/t/unable-to-get-any-data-wnt1-or-wnt10b-in-r-studio/311)
**Author:** [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\ **Replies:** 10\ **Last updated:** [July 21, 2022, 3:34pm UTC](https://help.c-moor.org/t/unable-to-get-any-data-wnt1-or-wnt10b-in-r-studio/311 "2022-07-21T15:34:52Z")
My R-Studio crashed and for some reason, I’m able to get most Wnt genes to plot their expression except for Wnt1 and Wnt10b, both of which are central to my poster. I brushed off the crash message thinking it was a regul… --- ## [Multiple Highest value points on top of UMAP](https://help.c-moor.org/t/multiple-highest-value-points-on-top-of-umap/305)
**Author:** [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\ **Replies:** 8\ **Last updated:** [July 20, 2022, 11:33pm UTC](https://help.c-moor.org/t/multiple-highest-value-points-on-top-of-umap/305 "2022-07-20T23:33:51Z")
Hi @mmccoy, I was able to graph out a Umap with the highest value points alongside the regular Umaps. I was only able to get one though because whenever I ran the code with two I got this message. I also got thes… --- ## [What embryonic stage/day is covered in the Mixed gastrulation and full data set we are provided through the R](https://help.c-moor.org/t/what-embryonic-stage-day-is-covered-in-the-mixed-gastrulation-and-full-data-set-we-are-provided-through-the-r/307)
**Author:** [@ShamounDivanyan](https://help.c-moor.org/u/ShamounDivanyan)\ **Replies:** 2\ **Last updated:** [July 19, 2022, 3:51pm UTC](https://help.c-moor.org/t/what-embryonic-stage-day-is-covered-in-the-mixed-gastrulation-and-full-data-set-we-are-provided-through-the-r/307 "2022-07-19T15:51:24Z")
What specific “time frame” are we given in the development of the mouse embryo? What I really need to know is what stages the data set is started on and cut off at? --- ## [Binding Sites in Transcription Factors](https://help.c-moor.org/t/binding-sites-in-transcription-factors/302)
**Author:** [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\ **Replies:** 4\ **Last updated:** [July 14, 2022, 7:36pm UTC](https://help.c-moor.org/t/binding-sites-in-transcription-factors/302 "2022-07-14T19:36:29Z")
Hi @LindsayHayes , I was told to ask you about looking for binding sites between two genes, mine being Wnt6 and Elf5. I don’t remember how to do that so I was wondering if you could remind me how to. (Sorry if this is ba… --- ## [Making a QR code](https://help.c-moor.org/t/making-a-qr-code/297)
**Author:** [@yanethp](https://help.c-moor.org/u/yanethp)\ **Replies:** 1\ **Last updated:** [July 8, 2022, 9:54pm UTC](https://help.c-moor.org/t/making-a-qr-code/297 "2022-07-08T21:54:24Z")
Is it possible to make a QR code for my R notebook to put on my Research Poster? --- ## [Help on R code to identify specific cells expressing lefty1 or lefty2](https://help.c-moor.org/t/help-on-r-code-to-identify-specific-cells-expressing-lefty1-or-lefty2/274)
**Author:** [@yanethp](https://help.c-moor.org/u/yanethp)\ **Replies:** 1\ **Last updated:** [June 17, 2022, 3:01pm UTC](https://help.c-moor.org/t/help-on-r-code-to-identify-specific-cells-expressing-lefty1-or-lefty2/274 "2022-06-17T15:01:59Z")
@mmccoy @LindsayHayes @cpozmanter Last semester I analyzed the gene expression of Lefty1 and Lefty2. I focused on the differential expression of each within celltypes and found that they were both expressed in the defin… --- ## [Cellxgene not in list of Compute Images](https://help.c-moor.org/t/cellxgene-not-in-list-of-compute-images/270)
**Author:** [@ShamounDivanyan](https://help.c-moor.org/u/ShamounDivanyan)\ **Replies:** 2\ **Last updated:** [June 14, 2022, 5:37pm UTC](https://help.c-moor.org/t/cellxgene-not-in-list-of-compute-images/270 "2022-06-14T17:37:58Z")
cellxGene is not showing up when I try to create a new container in sciserver. --- ## [Help On Wesbite](https://help.c-moor.org/t/help-on-wesbite/233)
**Author:** [@yanethp](https://help.c-moor.org/u/yanethp)\ **Replies:** 4\ **Last updated:** [May 9, 2022, 5:59pm UTC](https://help.c-moor.org/t/help-on-wesbite/233 "2022-05-09T17:59:42Z")
I am getting this error code for my Github website [Next page](https://help.c-moor.org/c/help/7.md?page=1)