neurogenomics rare_disease_celltyping issues

neurogenomics / rare_disease_celltyping

Code, data and results associated with the "Rare diseases cell-typing" project.

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Include animal model availability in target prioritisation pipeline

#71 bschilder opened 1 month ago
0
Move AD/PD networks to supplementary materials

#70 bschilder opened 1 month ago
1
Target prioritisation pipeline figure

#69 bschilder opened 1 month ago
0
Assess distribution of congenital phenotypes

#68 bschilder opened 1 month ago
0
Rework target prioritisation figure

#67 bschilder closed 1 month ago
1
Adjust ontology levels figure

#66 bschilder opened 1 month ago
4
Create static versions of network plots

#65 bschilder closed 1 month ago
0
Redo Monarch recall stats

#64 bschilder closed 1 month ago
1
Remove diagnosis/prognosis figures

#63 bschilder opened 1 month ago
0
Adjust congenital onset figure

#62 bschilder closed 1 month ago
1
Remake equations with color coding

#61 bschilder closed 2 months ago
1
Rewrite manuscript

#60 bschilder closed 1 month ago
2
Regenerate manuscript figures with new results

#59 bschilder closed 3 months ago
2
Assess our results against known phenotype-celltype links

#58 bschilder closed 4 months ago
4
Update website with the results from the new scRNA-seq datasets

#57 NathanSkene closed 4 months ago
1
Identify variant-level mechanisms of each rare disease

#52 bschilder closed 5 months ago
3
`phenomix`: Exploring more efficient methods for celltype enrichment

#51 bschilder closed 1 month ago
5
Assess pLI in HPO genes

#50 bschilder opened 6 months ago
6
Describe Human Cell Landscape CTD levels

#49 bschilder closed 6 months ago
2
Recreate entire study in one Rmarkdown

#48 bschilder closed 2 months ago
2
Are congenital phenotypes more enriched for fetal cell types?

#47 bschilder closed 3 months ago
4
Engage with rare disease community

#46 bschilder opened 1 year ago
2
Find regulator genes

#45 bschilder opened 1 year ago
2
In Fig 3a,b,c, remove the "other" line... it isn't required and isn't really in contrast to the phenotypes

#44 NathanSkene closed 1 year ago
1
For the recurrent infection plots, set scale_y=free

#43 NathanSkene closed 6 months ago
3
Make this plot with log(fold change) to reduce effect of outliers

#42 NathanSkene closed 2 years ago
1
Figures must be legible when reduced to 5.5cm or 12cm wide, with resolution of 150 to 300 dots per inch (dpi)

#41 NathanSkene closed 6 months ago
1
Cut the words in the paper back to 2500 to fit with requirements for science report submission

#40 NathanSkene closed 1 year ago
5
Group plots into larger figures

#39 bobGSmith closed 1 year ago
5
Dev descartes

#38 bobGSmith closed 2 years ago
0
Currently when looping through the phenotypes, it crashes and has to be restarted whenever there is an error (e.g. not enough genes in the list). Add try-catch statements and make a log record.

#37 NathanSkene closed 2 years ago
1
Cleanly separate functions from scripts + ensure all functions pass dev::check()

#36 NathanSkene closed 1 year ago
13
Look into use of Snakemake for the make file: could it also be used in place of the EWCEwrapper functions?

#35 NathanSkene closed 6 months ago
1
Replace rda files with rds

#34 bschilder closed 2 years ago
0
Improve function coding practices

#32 bschilder closed 1 year ago
3
Improve app speed

#31 bschilder closed 1 year ago
2
Add the markdown document of MSc Report to the github repo so we can start editing that

#29 NathanSkene closed 2 years ago
1
Document all the functions in Roxygen style https://github.com/ovrhuman/RD_EWCE_Website_and_apps

#28 NathanSkene closed 2 years ago
1
Show that cell type enrichments become purer as you move towards leaf nodes

#27 NathanSkene closed 1 year ago
13
Cell_select_interactive: `Error:`loops` is `FALSE`, but `x` contains loops. `

#26 bschilder closed 1 year ago
8
Add some graphs showing the range of ontology terms associated with some cell types

#25 NathanSkene closed 1 year ago
4
Graphs showing relationship between celltype enrichment strengths + ontology level, should use violin plots

#24 NathanSkene closed 1 year ago
2
Setup the document so that the text can be edited in authorea + figures regenerated from a markdown file

#23 NathanSkene closed 1 year ago
1
Make figures / text based around the cell type specificity of obvious facial markers visible from birth

#21 NathanSkene closed 1 year ago
5
There's a list of ~400 phenotypes that didn't run succesfully. Bobby thinks it's because of e.g. hyphens in the name. Need to figure out why this was and get them working.

#20 NathanSkene closed 1 year ago
1
Merge dev_descartes into master (this has Bobby's make file & CTD dir removed etc)

#19 NathanSkene closed 1 year ago
0
Does the likelihood of a phenotype being associated with multiple cell types increase as you move up the HPO ontology?

#18 NathanSkene closed 1 year ago
1
Create a makefile that runs the whole analysis from scratch

#17 NathanSkene closed 1 year ago
5
Work with Alan Murphy to move `RunEWCE` and `EWCEWrapper` into the main EWCE package

#16 NathanSkene closed 6 months ago
1
Setup a better project folder structure

#15 NathanSkene closed 2 years ago
3