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Fix Dropout #17

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Fix Dropout #17

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ef91690
fixed import issues, added 'sensitivity' submodule
cooperlab Aug 9, 2016
75255bb
changed max step size back to 1
Aug 12, 2016
3e6a517
Merge pull request #7 from cooperlab/nandebug
safooray Aug 12, 2016
31df3f3
added model analysis functions
cooperlab Aug 16, 2016
67ea239
Fixed dimensionality issues with numpy matrices versus arrays
cooperlab Aug 16, 2016
f97b62e
added clustering functionality
cooperlab Aug 17, 2016
21f0bcd
Merge branch 'sensitivity' of https://github.com/cooperlab/SurvivalNe…
Aug 17, 2016
a320dfe
Update RiskCluster.py
Aug 17, 2016
3c8acda
Added GSEA-related functions.
cooperlab Aug 18, 2016
5cfe9e8
Revert "Added GSEA-related functions."
cooperlab Aug 18, 2016
760d1f7
Converted to matplotlib. Added KM and ScatterPair functions.
cooperlab Aug 19, 2016
4dc87b7
Updated submodule name to "analysis".
cooperlab Aug 19, 2016
d27dc06
Moved matrix conversion into function.
cooperlab Aug 19, 2016
cf7f54d
Added stdout messaging. Removed unused input parameter. Reduced defau…
cooperlab Aug 19, 2016
0ef86de
Fixed imports, added docstrings.
cooperlab Aug 19, 2016
fc5d28f
Merge pull request #13 from cooperlab/matplotlib
Aug 19, 2016
6a1afdb
Update Visualize.py
Aug 21, 2016
b9dea69
Update RiskCluster.py
Aug 21, 2016
1e43fe1
Delete PlotRanked.py
Aug 22, 2016
53af236
Delete Visualize.py
Aug 22, 2016
85585e6
Create Visualization.py
Aug 22, 2016
242e243
Create PathwayAnalysis.py
Aug 22, 2016
de9b179
Create FeatureAnalysis.py
Aug 22, 2016
2ad7021
Create ReadGMT.py
Aug 22, 2016
e715904
Create SSGSEA.py
Aug 22, 2016
7d0ccca
Update __init__.py
Aug 22, 2016
955efeb
Merge pull request #14 from cooperlab/refactor
Aug 22, 2016
dcb51d7
Update __init__.py
Aug 23, 2016
dd9240f
Fixed KM plots for empty values
cooperlab Aug 27, 2016
76512b6
Fixed track colors for CNV values
cooperlab Aug 27, 2016
1c272c0
Exposed plot numbers for each plot type as parameter
cooperlab Aug 27, 2016
3bcbe7e
Added functions for writing gradients to disk for GSEA/SSGSEA
cooperlab Sep 12, 2016
9d4c8c0
Removed GSEA function - use GenePattern instead
cooperlab Sep 12, 2016
5a3ea40
fixed normalization of risk gradients
cooperlab Mar 27, 2017
74797ee
Update README.md
safooray Apr 22, 2017
d14fed0
Update README.md
safooray Apr 22, 2017
0646090
Update README.md
safooray Apr 22, 2017
3d369a2
merge experiment with master
safooray Apr 22, 2017
043d373
fix analysis according to dropout fix
safooray Apr 23, 2017
cf24585
fix analysis according to dropout fix
safooray Apr 23, 2017
8cb9661
organized examples
safooray Apr 23, 2017
1912919
organize usage
safooray Apr 24, 2017
cc60d3e
Update README.md
safooray Apr 24, 2017
ed9a79d
Merge pull request #18 from CancerDataScience/cleanup
safooray Apr 24, 2017
824045c
Delete run.sh
safooray Apr 24, 2017
83ebf9c
Delete train_set
safooray Apr 24, 2017
585bcbd
Delete val_set
safooray Apr 24, 2017
da98b3d
update git ignore
safooray Apr 24, 2017
142ccc9
Merge branch 'cleanup' of https://github.com/cooperlab/survivalnet in…
safooray Apr 24, 2017
8433970
update .gitignore
safooray Apr 24, 2017
7c24a6f
Update README.md
safooray Apr 24, 2017
9e93090
Merge pull request #19 from CancerDataScience/cleanup
safooray Apr 24, 2017
dabf3aa
Create x
safooray Jul 21, 2017
f19ab52
Added example dataset.
safooray Jul 21, 2017
491def2
Delete x
safooray Jul 21, 2017
2ec5d75
fixed Run.py
safooray Aug 22, 2017
005902d
fixed Run.py
safooray Aug 22, 2017
66fafb2
fixed constants in Run.py
safooray Aug 22, 2017
90cdf6a
String concat cleanup
safooray Aug 22, 2017
b11fc15
cleanup and doc
safooray Aug 22, 2017
e46c2d1
added docstrings
safooray Aug 23, 2017
b14a206
Update README.md
safooray Aug 23, 2017
fd65500
Update README.md
safooray Aug 23, 2017
3c50673
Update README.md
safooray Aug 23, 2017
0bbbdea
error fix
safooray Aug 30, 2017
a7f8ccd
Merge branch 'master' of https://github.com/CancerDataScience/Surviva…
safooray Aug 30, 2017
e68bd1e
removed scipy code
safooray Aug 30, 2017
010654e
removed LineSearch class
safooray Aug 30, 2017
98928f0
Adding Docker Image Installation guidelines
cramraj8 Aug 31, 2017
3de20ae
model cleanup
safooray Aug 31, 2017
b05cc54
model cleanup
safooray Aug 31, 2017
d4761ec
model cleanup
safooray Aug 31, 2017
0452f43
Modified Documentation
cramraj8 Aug 31, 2017
708acc6
Merge pull request #22 from CancerDataScience/docket-installatoin-guide
safooray Aug 31, 2017
3b5a0f0
Update LICENSE
Aug 31, 2017
94e6a28
Update README.md
Aug 31, 2017
57d6175
Changing the Docker Cloud repository name.
cramraj8 Sep 5, 2017
c9bab5e
Update README.md
Sep 5, 2017
3ad3764
Update README.md
Sep 5, 2017
6fec30c
changed the docker cloud repo name and link
cramraj8 Sep 5, 2017
b7865c0
error fix
safooray Sep 6, 2017
cbf8c56
save model
safooray Sep 6, 2017
210495c
Simplification
safooray Sep 6, 2017
7917d42
added requirements
safooray Sep 6, 2017
9620031
Update README.md
safooray Sep 6, 2017
890eb88
Merge pull request #24 from CancerDataScience/analysis-fix2
Sep 6, 2017
d266319
Merge branch 'master' into documentation
Sep 6, 2017
5c23be8
Merge pull request #23 from CancerDataScience/documentation
Sep 6, 2017
0db3eec
Merge pull request #26 from CancerDataScience/requirements
Sep 6, 2017
ea69044
Update README.md
Sep 7, 2017
ad54772
Merge branch 'master' into analysis-fix
safooray Sep 8, 2017
1a00b08
Merge pull request #15 from CancerDataScience/analysis-fix
safooray Sep 8, 2017
0cf354d
fixed analysis init and function call in ModelAnalysis
safooray Sep 9, 2017
0608f42
Merge pull request #27 from CancerDataScience/glioma-model-analysis
safooray Sep 9, 2017
da27410
added final model
safooray Sep 12, 2017
c5b498a
added final model
safooray Sep 12, 2017
de26567
Merge pull request #28 from CancerDataScience/dtype-error-fix
safooray Sep 12, 2017
ad9ff1b
Update README.md
safooray Oct 19, 2017
83b99ff
Update README.md
safooray Oct 19, 2017
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5 changes: 1 addition & 4 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,4 @@ output/
build
dist
*.egg-info
Run.py
panorg_Run.py
Cost_Function.py
Bayesian_Optimization.py
*.out
53 changes: 0 additions & 53 deletions Bayesian_Optimization.py
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295 changes: 0 additions & 295 deletions CostFunction.py
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