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https://hbctraining.github.io/DGE_workshop_salmon_online/lessons/10_FA_over-representation_analysis.html When working with my own data set, when running the cnetplot code I get this warning: ``` Scale for size is already present. Adding another scale for size, which...
``` gseaKEGG
No error. Just does not produce any graph ``` > pathview(gene.data = foldchanges, + pathway.id = "hsa03008", + species = "hsa", + limit = list(gene = 2, # value gives...
degCovariates produces a graph and outlines significant results, but does not actually shade graph based on r correlation value. This is despite R values being non-zero. I tried replacing the...
There seems to be some debate about whether IgG or chromatin input is best for negative control in Cut and Run. A quick google seems to suggest that most people...
The following problem exists for at least exercises from day 2: Exercises from the self learning section, https://hbctraining.github.io/Intro-to-R-flipped/schedules/links-to-lessons.html need to be updated to match what is presented as takehome material...
In https://hbctraining.github.io/scRNA-seq_online/lessons/09_merged_SC_marker_identification.html adding annotations in the loop using the following method results in a many-to-many warning (when using methods to download annotations using annotationHub). This is because `unique(annotations[, c("gene_name", "description")])`...
- positional param loop section: add explicit statement to `cd raw_fastq` before writing loop script - long exercise in positional params: for some reason all questions are labeled as "1."...
In https://github.com/hbctraining/Intro-to-rnaseq-hpc-salmon-flipped/blob/main/lessons/04b_data_organization.md, section titled "Implementing data management best practices", there is a hyperlink "In a previous lesson" which is broken.
Apparently the link is broken because Horvath left UCLA and is no longer paying for the website Our best bet is to probably replace with internet archive link to the...