Radhika Khetani

Using SCT for marker ID

2

https://search.r-project.org/CRAN/refmans/Seurat/html/PrepSCTFindMarkers.html Questions in class: "Why do we set the default assay to "RNA" prior to FeaturePlot? Why do we use NormalizeData prior to FeaturePlot? Wasn't the data normalized in the...

update the notes about doublet detection in QC

Currently this lesson uses a park ranger log as a input data, would be good to convert it to a metadata file instead, in the future. https://github.com/hbctraining/Training-modules/blob/master/Intermediate_shell/lessons/AWK_module.md

Topics in development

2

- [ ] 1. Salmon/sleuth (Prereq: familiarity with HPC, bash and R) - [x] 2. SRA/GEO data download (Prereq: familiarity with HPC and bash) - [ ] 3. Sequence data...

``` gseaKEGG

Someone requested closed captioning last time, what options are available?

"Using Docker for reproducibility (R code)" https://hub.docker.com/r/rocker/rstudio

Update the following exercise to have a cleaner output enabling students to check it against the instructor's output. Remove the Bonus question. ```Do each of the following using a single...

HPC lesson updates and clarifications from Kathleen

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- data storage & memory on O2 are in units using base 2, not units using base 10 (e.g. tebibytes not terabytes. TiB = 1024 GiB, TB = 1000 GB)....