greenelab pancancer-evaluation issues

greenelab / pancancer-evaluation

Evaluating genome-wide prediction of driver mutations using pan-cancer data

BSD 3-Clause "New" or "Revised" License

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Optimizations for cross-cancer experiment scripts

#34 jjc2718 closed 4 years ago
0
Cross-cancer prediction experiments

#33 jjc2718 closed 4 years ago
1
Coefficient stability: gene dropout/pathway aggregation experiments

#32 jjc2718 opened 4 years ago
1
Model coefficient stability analysis

#31 jjc2718 closed 4 years ago
0
Remove relevant cancer type experiments + analysis

#30 jjc2718 closed 4 years ago
0
Add script to analyze coefficients of model fits

#29 jjc2718 closed 4 years ago
0
Faster recognition of experiments that have already run (or skipped)

#28 jjc2718 opened 4 years ago
0
Make it easier to run experiments for multiple random seeds

#27 jjc2718 closed 4 years ago
1
Cancer type classification experiments: train pan-cancer without X, test X

#26 jjc2718 closed 4 years ago
1
Make running experiments for multiple seeds easier

#25 jjc2718 closed 2 years ago
0
Separate data loading from model training + add model tests

#24 jjc2718 closed 4 years ago
0
Look into pan-cancer coefficients for cancer type

#23 jjc2718 opened 4 years ago
1
Fix cross-validation order bug

#22 jjc2718 closed 4 years ago
1
Analysis of held-out cancer type classification results

#21 jjc2718 closed 4 years ago
0
Stratified cross-validation experiments/visualizations

#20 jjc2718 closed 4 years ago
1
PCA of individual cancer types

#19 jjc2718 opened 4 years ago
0
Do highly mutated examples from explore_data script make sense?

#18 jjc2718 opened 4 years ago
0
Add script to do exploratory data analysis on TCGA data

#17 jjc2718 closed 4 years ago
1
Separate data loading and model training/evaluation

#16 jjc2718 closed 4 years ago
0
Add statistical testing to compare single-cancer and pan-cancer results

#15 jjc2718 opened 4 years ago
1
Refactor data loading code to load data once for multiple experiments

#14 jjc2718 closed 4 years ago
0
Save/load expression data as pickled dataframe instead of tsv file

#13 jjc2718 opened 4 years ago
0
Change gene_features bool array to use built-in Pandas annotations

#12 jjc2718 opened 4 years ago
0
Add general logging functionality

#11 jjc2718 opened 4 years ago
0
Subset gene features by MAD and clean up data preprocessing code

#10 jjc2718 closed 4 years ago
0
How many genes pass our imbalance filter?

#9 jjc2718 closed 4 years ago
0
Mutation burden prediction

#8 jjc2718 opened 4 years ago
0
Refactor classification script so data only gets loaded once

#7 jjc2718 closed 4 years ago
0
Add script to run pancancer classification experiments

#6 jjc2718 closed 4 years ago
1
Fix cancer type covariate when single cancer is held out

#5 jjc2718 closed 4 years ago
0
Cross-validation for imbalanced label case

#4 jjc2718 opened 4 years ago
2
Revisit file path configuration

#3 jjc2718 opened 4 years ago
0
Implement subsetting genes by MAD

#2 jjc2718 closed 4 years ago
1
Implement and test single-cancer cross-validation

#1 jjc2718 closed 4 years ago
1