Intro-to-peak-analysis
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hbctraining
An introduction to various methods/approaches for the analysis of peaks generated from ChIP-seq / CUT&RUN / ATAC-seq
See: https://github.com/hbctraining/Investigating-chromatin-biology-ChIPseq/issues/67 Maybe need to tweak any commands on how we got to a certain point.
IGV downloads are wonky. It might need ot be set dl=1, but it would be great if we can just build these file into the initial download probably.
People may need to install edgeR from bioconductor so add to packages to install
The GO terms might be outdated. When we re-ran edgeR we got like 800 fewer differentially DE peaks, so Upen updated it in the DE lesson, however, the terms probably...
Do we want use MEME? It didn't run in class Also, we need to add motif enrichment analysis (rather than novel motif, followed by motif comparison)
In the sample similarity lesson add a drop down on "when would I need tio implement a threshold" and show a plot where on sample drops off in enrichment (meeta/heather...
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An introduction to various methods/approaches for the analysis of peaks generated from ChIP-seq / CUT&RUN / ATAC-seq