scRNA-seq_online
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hbctraining
Hi All! I wasn't sure if you had seen that Seurat now has a function for aggregating to the sample level for pseudobulk DE analysis. Using a few functions as...
I'm working my way through lesson 6. I can't seem to find the Rdata file "cycle.rda" in the repo. I am looking in the wrong place? Cheers, Chris
Once you have run: ``` # Filter out low quality cells using selected thresholds - these will change with experiment filtered_seurat = 500) & (nGene >= 250) & (log10GenesPerUMI >...
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")])`...
Update code and associated images in the scRNA-seq repo ; specifically some UMAPs in clustering QC lesson
Hi，I have just learned the scRNA-seq_online course，I have a question when you visualiza the UMI counts (transcripts) per cell by code as bellow: # Visualize the number UMIs/transcripts per cell...
Check "Resources" section on scRNA-seq schedule page. Some broken links. Also, link the new DBMI materials for using R and RStudio on O2
We should add exercises which require more thinking and applying rather than just running code (feedback from surveys)
Add a troubleshooting section and review frequently encountered issues Day 2 qnd Day 3 classes tend to end early - we could afford to add some materials
I am confused about this, but the idea is whether we are normalizing too much or too little.
