TODO Reporting Summary Form

Need to fill out reporting summary form for paper with Molly

• Wants us to report one-sided or two sided and the name of the statistical test used
  • Is citing the tool used good enough?
    • GTeX
    • RELI
    • Homer
• Full description of the statistical parameters including central tendency?
  • Are the figures good enough (1C and 5A) or do we need to list the medians?
• Need Sex and source for all cell lines (used in the study?)
  • Also need authentication method?
    • Do we even do this?
  • Supplementary table 11
• Need replicate information for ChIP-seq

DONE Find threshold to remove weird samples (pairwise reli) ARCHIVE

DONE Alzheimer's disease examination ARCHIVE

DONE Finish first draft of manuscript [2/2] ARCHIVE

DONE Extra Analysis ARCHIVE

DONE Unify genesets [1/1] ARCHIVE

Figure 1

DONE Create UMAP and PCA (Part B) [3/3] ARCHIVE

Figure 2

DONE Percent ChIP peaks (Part C) [1/1] ARCHIVE

DONE GREAT analysis (Part D) [6/7] ARCHIVE

Figure 3

DONE Part A [1/2] ARCHIVE

DONE SPAMO analysis (Part C) ARCHIVE

Figure 4 [2/2]

DONE Phenotype RELI (Part A) [3/3] ARCHIVE

DONE Mario Analysis ARCHIVE

Nextflow Pipeline

DONE Dockerize/Nixify R dependencies ARCHIVE

DONE Draft Methods ARCHIVE

DONE Browser sessions ARCHIVE

Papers to Read

DONE Harley et al ARCHIVE

DONE Figure 5 ARCHIVE

DONE Figure 6 ARCHIVE