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Sage-Bionetworks
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NF_LandscapePaper_2019
This repository hosts all the code used to generate analyses and figures for the landscape paper
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Brainstorm visualization of RF trees
#63
sgosline
closed
4 years ago
0
Add PCA to Fig 1 analysis and create Fig 2
#62
sgosline
closed
4 years ago
2
gsea enrichment of metaviper gene sets
#61
allaway
closed
4 years ago
2
Fig1 and table 1
#60
sgosline
closed
4 years ago
0
adding ensemble rf for LVs
#59
jaybee84
closed
4 years ago
1
LV-metaViper fix
#58
sgosline
closed
4 years ago
1
Added metaviper correlations for important lvs
#57
sgosline
closed
4 years ago
1
RF cibersort closes #37
#56
jaybee84
closed
4 years ago
1
README updates
#55
sgosline
closed
4 years ago
0
Random forest using MCP counter scores as input
#54
jaybee84
closed
4 years ago
2
run metaviper correlation with all LVs and store in table
#53
sgosline
closed
4 years ago
3
Update README.md
#52
jaybee84
closed
4 years ago
1
Tested the correlation b/w LVs and metaviper proteins.
#51
sgosline
closed
4 years ago
0
Redo analysis for LVs
#50
allaway
closed
4 years ago
2
LV Drug KS test
#49
allaway
closed
4 years ago
1
Create immune classifier table on syn21046734
#48
sgosline
closed
4 years ago
1
updated lvs to include cbttc and lockfile to incl plier
#47
allaway
closed
4 years ago
0
init renv for this project
#46
allaway
closed
4 years ago
1
add renv so we are all working with the same versions of packages?
#45
allaway
closed
4 years ago
3
redo LV analyses and analyses dependent on this with CHOP pNF data added
#44
allaway
closed
4 years ago
2
Split LVs by mutation to test for significance.
#43
sgosline
closed
4 years ago
1
Adding random forest classification using latent variables (closes: #36)
#42
jaybee84
closed
4 years ago
1
ks test/gsea for enrichment of drugs in lvs
#41
allaway
closed
4 years ago
1
Update README.md
#40
allaway
closed
4 years ago
0
Nothing is significant, but I find the plots useful, and can be handy…
#39
sgosline
closed
4 years ago
2
updated code to remove glioma data
#38
sgosline
closed
4 years ago
0
Run random forest with pathway info for genes
#37
jaybee84
closed
4 years ago
1
Run random forest analysis with LV data
#36
jaybee84
closed
4 years ago
0
Remove glioma from metaviper correlation
#35
sgosline
closed
4 years ago
1
Repeat tumor immune heatmaps without LGG
#34
sgosline
closed
4 years ago
0
Repeat tumor immune analysis without gliomas
#33
sgosline
closed
4 years ago
0
Look for immune signatures that are correlated with patient age
#32
sgosline
closed
4 years ago
1
add kw test experiment for all lvs
#31
allaway
closed
4 years ago
1
Update README.md
#30
allaway
closed
4 years ago
1
comparison of pNF vs MPNST to identify interesting LVs
#29
allaway
closed
4 years ago
0
cmap on nf samples
#28
allaway
closed
4 years ago
1
correlate lv expression with metaviper expression?
#27
allaway
closed
4 years ago
1
create table 1
#26
allaway
closed
4 years ago
0
Found specific cell types measurements by gene mutation
#25
sgosline
closed
4 years ago
1
fix duplication of cnf lvs
#24
allaway
closed
4 years ago
1
Small sample size but immune cell differences in NFs
#23
sgosline
closed
4 years ago
0
Enable github.io - make readme links go to rendered notebooks by default
#22
cgreene
closed
4 years ago
7
add 09 nb - cnf itching vs LVs
#21
allaway
closed
4 years ago
0
Does this repo need to be private?
#20
allaway
closed
4 years ago
4
Update README.md
#19
allaway
closed
4 years ago
0
Did some quick cNF-immune tests
#18
sgosline
closed
4 years ago
1
evaluate the NF-high LVs correlation to expression in recount2
#17
allaway
closed
4 years ago
11
evaluate cNF clinical characteristics vs expression signatures
#16
allaway
closed
4 years ago
2
adding immune - lv correlations
#15
allaway
closed
4 years ago
2
ADded in some cNF gene expression correlations.
#14
sgosline
closed
4 years ago
2
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