TODO RNA-seq
- Find DEGs relative to control by celltype (Flp vs TREX), then protein (E proteins) for each strain.
- K means cluster heatmap of DEGs
- Linkage cluster heatmap of DEGs
- Spark plots
- Deseq2 code: https://tfinternal.research.cchmc.org/gitlab/mixtape_pipelines/pipelines/differential-expression-rnaseq/-/tree/master/wrl-deganalysis/assets/report_templates/deseq2
TODO Pairwise RELI ChIP-seq [0/2]
- RELI each sample against each sample for each protein and celltype for each strain
- % Overlap heatmap
TODO Pairwise RELI ATAC-seq
- RELI each sample against each sample for each protein and celltype for each strain
- % Overlap heatmap
Preparing the data and QC
Data freeze of all samples should be done before analysis begins
TODO ask Andrew anatomy about the RNA-seq differential analysis pipeline outputs
- Send email to PHil, Lee and Andrew
- Run1 vs run2
Check RNA-seq directory for Differential analysis directory
PCA/UMAP [0/1]
-
[-] Create PCA and UMAP code
- [X] Fix ChIP seq label on ATAC plots
- [X] Add percentage of variance for PCA
- Confirm failed enumber is no longer in metadata
- [X] Initial Implementation
DONE get data from Phil ARCHIVE
DONE Does Phil Have A nextflow pipeline for EBV? ARCHIVE
Reading
TODO Read EBV manuscript
- a good template
TODO Review VTR Paper to read
https://pubmed.ncbi.nlm.nih.gov/32649876/