neurogenomics/RareDiseasePrioritisation

Issues

• Consider adjusting weights of each severity metric

  #38 opened 4 months ago by bschilder
  0

• Update quarto file and render html

  #36 opened 4 months ago by bschilder
  0

• Write initial draft of HPO GPT annotations manuscript

  #31 opened 5 months ago by bschilder
  11

• Check counts for on-target validation plot

  #35 opened 6 months ago by bschilder
  1

• Assess existence of experimental models

  #33 opened 6 months ago by bschilder
  15

• Assess whether cell types predict clinical course

  #23 opened 6 months ago by bschilder
  9

• Repeat symptom-level enrichment analyses using EWCE

  #25 opened 6 months ago by bschilder
  1

• Annotate diseases/phenotypes using chatGPT

  #19 opened 9 months ago by bschilder
  18

• Repeat phenotype-level enrichment analyses using EWCE

  #29 opened 9 months ago by bschilder
  19

• Filter by frequency

  #34 opened 9 months ago by bschilder
  3

• Generate table of all phenotypes ranked by GPT-annotated severity

  #32 opened 10 months ago by bschilder
  1

• Prioritise therapeutic candidates for nervous system phenotypes

  #30 opened 10 months ago by bschilder
  1

• Are all the cell types targeted in clinical trials temrinally differentiated?

  #14 opened 2 years ago by momokootani
  1

• Hypergeometric test

  #11 opened 2 years ago by momokootani
  0

• HPO terms equivalent to each tier

  #12 opened 2 years ago by momokootani
  1

• Targets for AAVs

  #13 opened 2 years ago by momokootani
  1

• Genes associated with phenotypes

  #9 opened 2 years ago by momokootani
  1

• Gene associations

  #10 opened 2 years ago by momokootani
  0

• Prepare cardio results

  #28 opened a year ago by bschilder
  1

• Access to full data from OMIM/DECIPHER/Orphanet

  #26 opened a year ago by bschilder
  1

• Add evidence scores to gene associations

  #27 opened a year ago by bschilder
  4

• Identify neurodegeneration-related results

  #21 opened a year ago by bschilder
  0

• Investigate the intersection between dementia/neurodegeneration vs. diabetes/dementia

  #22 opened a year ago by bschilder
  1

• Adjust filtering parameters

  #17 opened a year ago by bschilder
  7

• Filter based on disease-level

  #18 opened a year ago by bschilder
  8

• Generate report on the number of HPO disease modifiers

  #20 opened a year ago by bschilder
  5

• Replicate Momoko's analyses with code

  #15 opened 2 years ago by bschilder
  1

• Add rmarkdown report

  #16 opened 2 years ago by bschilder
  1

• How can we systematically say "is this targetable in adulthood?". E.g. short femur is not targetable with gene therapy... not having a heart attack is targetable

  #6 opened 2 years ago by NathanSkene
  1

• Read about OMIM and HPO... understand the data that's in there... how does it get there? Can it be used to infer prevalence in any way?

  #7 opened 2 years ago by NathanSkene
  1

• Get a spreadsheet with all phenotype and celltype associations

  #8 opened 2 years ago by NathanSkene
  2

• Is there any quantification of the severity of a phenotype? E.g. death is worse than being short.

  #5 opened 2 years ago by NathanSkene
  1

• How can we get data on the prevalence of a particular phenotype?

  #4 opened 2 years ago by NathanSkene
  4

• Read Bobby's report and understand the data that we have

  #2 opened 2 years ago by NathanSkene
  1

• Understand why AAV's are better for targeting some cell types than others: select which of our cell types are best candidates for gene therapy

  #1 opened 2 years ago by NathanSkene
  1

• Understand how to use the data portal that Bobby developed

  #3 opened 2 years ago by NathanSkene
  1

• Explain methods diagrammatically

  #24 opened a year ago by bschilder
  4