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matsengrp
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samm
Survival analysis of mutation motifs
GNU General Public License v3.0
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slightly changed partis call
#332
dunleavy005
closed
5 years ago
0
changed # of mutations drawn to account for all sites
#331
dunleavy005
closed
5 years ago
0
simulate naive_seq from partis
#330
dunleavy005
closed
5 years ago
1
argparse comment fix
#329
dunleavy005
closed
5 years ago
0
made simulate_shm_on_given_tree.py for multiple trees
#328
dunleavy005
closed
5 years ago
0
more shm treesim changes
#327
dunleavy005
closed
5 years ago
2
added human heavy-chain S5F data
#326
dunleavy005
closed
5 years ago
0
Null and saturated models
#325
dawahs
opened
6 years ago
0
Residual and coef plots
#324
dawahs
opened
6 years ago
0
Position features
#323
dawahs
closed
6 years ago
0
Immunomotif updates
#322
dawahs
closed
6 years ago
0
Multiple mutation scripts
#321
jjfeng
closed
6 years ago
0
Update imputed code
#320
dawahs
closed
6 years ago
0
Update shazam vs samm comparison for real data
#319
jjfeng
closed
6 years ago
1
Section 4 revisions
#318
dawahs
closed
6 years ago
0
use separate scratch dir for each cv fold
#317
jjfeng
closed
6 years ago
0
Figure 3 revisions
#316
dawahs
closed
6 years ago
0
Keep running EM iterations until hessian only has nonneg variance estimates
#315
jjfeng
closed
6 years ago
1
cvxpy version
#314
jfukuyama
opened
6 years ago
0
preprocess_data issue
#313
jfukuyama
opened
6 years ago
0
Get ready for running hedgehog plots
#312
jjfeng
closed
6 years ago
1
Minor updates for plotting simulated samm shazam logistic
#311
jjfeng
closed
6 years ago
0
add gizmo fix
#310
jjfeng
closed
6 years ago
0
Update germline simulator call
#309
dawahs
closed
6 years ago
0
Logistic: tune penalty params
#308
jjfeng
closed
6 years ago
0
revert to multiprocessing
#307
jjfeng
closed
6 years ago
0
Use cvxpy to solve logistic things instead
#306
jjfeng
closed
6 years ago
0
Fix aggregating bugs and run pipeline tests
#305
dawahs
closed
6 years ago
2
use neg log loss instead
#304
jjfeng
closed
6 years ago
0
Add logistic regression cause reviewer wants.
#303
jjfeng
closed
6 years ago
0
add CV where we get common support or refit to get new support
#302
jjfeng
closed
6 years ago
0
Adjacent motif features, and more generic feature generating
#301
dawahs
closed
6 years ago
2
Update submodules
#300
dawahs
closed
6 years ago
0
Document samm ranking utility
#299
dawahs
closed
6 years ago
1
Document SAMM ranking
#298
matsen
closed
6 years ago
2
Floating point zero
#297
krdav
closed
6 years ago
0
Calculating martingale residuals
#296
dawahs
closed
6 years ago
0
Edge cases in processing sequences
#295
dawahs
opened
6 years ago
0
Hessian speedup take 2
#294
dawahs
closed
6 years ago
2
Installation docs
#293
dawahs
closed
6 years ago
2
docs
#292
matsen
closed
6 years ago
0
Update private data paths in scons scripts and fitting code
#291
dawahs
closed
6 years ago
2
dependencies
#290
matsen
closed
6 years ago
0
use sparse matrix
#289
dawahs
closed
6 years ago
1
Create LICENSE
#288
dawahs
closed
6 years ago
0
Imputed ancestors update
#287
dawahs
closed
6 years ago
1
Fix likelihood bugs
#286
dawahs
closed
6 years ago
0
Absolute path
#285
krdav
closed
6 years ago
0
convert shazam to theta and get likelihood of ETE tree
#284
dawahs
closed
6 years ago
0
Make `fit_samm` an importable function.
#283
jjfeng
opened
6 years ago
0
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