Meeta Mistry

update the elbow plot

2

the elbow plot markdown (quantitave approach) needs a figure update

updates to FA lessons

1

remove things we don't use anymore ? SPIA Also add new visualizations (suggestions from @hwick's code)

newer approaches, methods? Remove some of the older methods we don't really use?

update image to say scratch3

1

might also need this in variant calling

Add multiQC snippet so people know that they can aggregate QC across samples.

In variant calling we use string manipulation `cd /n/scratch/users/${USER:0:1}/$USER` Can we include this in our automation lesson? https://github.com/hbctraining/variant_analysis/blob/main/lessons/01_data_organization.md#a-quick-explanation-on-the-use-of-user01

there is an image in the bowtie2 section (right under a section where we talk about soft-clipping) whihc is not relevant and difficult to explain. let's remove it and/or maybe...

add an image to represent the Seurat object

2

this will be helpful in the first lesson to understand how the slots/layers work. Also, we can reference it in the cheatsheet

Hello, I am using Seurat to analyze my Visium data, and have noticed dramatic differences between the SCT result between v4 and v5. Everything is detailed below - but my...

adding more on integrating data

1

not just with RNA-seq; but also other data like ATAC and using marks to find enhancer regions etc