UIUCSinhaLab GEMSTAT issues

UIUCSinhaLab / GEMSTAT

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

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Test that coop file and .par files agree on cooperativities.

#47 bryan-lunt opened 6 years ago
0
Create a tool to convert .par formats and free-fix format.

#46 bryan-lunt opened 6 years ago
0
Problem in Corr

#45 shounakbhogale opened 6 years ago
1
It was the ParFactory::load that was not creating enough/useful errors.

#44 bryan-lunt closed 6 years ago
2
Problem in coop parser (HALF_DIRECTIONAL)

#43 bryan-lunt opened 6 years ago
0
Default pars created by the ParFactory don't have interactions in new_storage branch.

#42 bryan-lunt closed 6 years ago
0
Fix return arguments in functions to use rvalue references.

#41 bryan-lunt opened 7 years ago
1
Additional Parameters

#40 bryan-lunt opened 7 years ago
1
Markov

#39 bryan-lunt closed 7 years ago
0
Add scripts/submodules to get SGL/NLOpt, and an option to fetch/build/link statically.

#38 bryan-lunt opened 7 years ago
1
Recreate IND gemstat using new "Conditions" and ExprFunc class hierarchy, as an example.

#37 bryan-lunt closed 6 years ago
1
cooprativity file parser is insufficiently strict.

#36 bryan-lunt opened 7 years ago
0
No example factor_info.txt file.

#35 bryan-lunt opened 7 years ago
0
The usenlopt branch throws an error if a starting point has values outside the optimization bounds?

#34 bryan-lunt opened 7 years ago
0
Memory Leak

#33 bryan-lunt closed 8 years ago
0
Merge separateModelConcern (and logistic regression) into master.

#32 bryan-lunt closed 8 years ago
0
Meaningless message if inputs incompatible with current model provided. (IE providing coop input for models where that is not needed.)

#31 bryan-lunt opened 8 years ago
0
No activators if no factor_info file provided.

#30 bryan-lunt opened 9 years ago
2
Incorrect sine-based infty_transform

#29 bryan-lunt closed 6 years ago
0
Bad exception handling in gradient_minimize .

#28 bryan-lunt closed 6 years ago
1
Merge the fix for factor threshold input in the MASTER branch.

#27 bryan-lunt closed 9 years ago
0
Merge the fix for factor threshold input in the IND branch.

#26 bryan-lunt closed 9 years ago
0
Fix mistake in which ExprPredictor.cpp was used in "designPatterns" branch.

#25 bryan-lunt closed 9 years ago
0
Carefully consider how const ExprPar& are used in ExprPredictor.cpp and INDExprPredictor.cpp, and how to fix that.

#24 bryan-lunt opened 9 years ago
1
In the master branch, somehow when the .par file is loaded, its factorThresholds are not loaded.

#23 bryan-lunt opened 9 years ago
0
pi parameter

#22 khajoue2 opened 9 years ago
1
Not all command-line arguments are documented.

#21 bryan-lunt opened 9 years ago
0
The free_fix (indicator_bool) parser code is broken.

#20 bryan-lunt closed 9 years ago
6
-et option (default factor threshold) and Hassan's factor thr file are (effectively) ignored.

#19 bryan-lunt closed 9 years ago
2
If no factorinfo file is provided, assume all factors are activators? (Or throw an error.)

#18 bryan-lunt opened 9 years ago
0
Eliminate superfluous copying of Sequences and similar variables.

#17 bryan-lunt opened 9 years ago
0
Autotest

#16 bryan-lunt closed 9 years ago
0
The free_fix (indicator_bool) file is not in an order that makes sense to users.

#15 bryan-lunt closed 6 years ago
1
Read optimization bounds from another input file.

#14 bryan-lunt closed 7 years ago
1
Make Sequence objects know their own names, eliminate seqNames arrays anywhere they are used.

#13 bryan-lunt opened 9 years ago
1
Document that IND GEMSTAT is sensitive to TF order

#12 bryan-lunt closed 9 years ago
0
Eliminate the need to input true expression when making a predition only.

#11 bryan-lunt opened 9 years ago
1
Make ExprPredictor::optimize_beta obey both constraints on beta and free_fix

#10 bryan-lunt opened 9 years ago
1
IND Gemstat is sensitive to the order of TFs, (and who knows what else?)

#9 bryan-lunt opened 9 years ago
2
Change optimization constraint enforcement to use sine/arcsine

#8 bryan-lunt closed 7 years ago
0
Fix the ExprPar::load function

#7 bryan-lunt opened 9 years ago
2
Remove need for cooperativity file. (put it into par.)

#6 bryan-lunt opened 9 years ago
0
Make the ExprPredictor objective functions a Strategy pattern.

#5 bryan-lunt closed 6 years ago
1
Need unit/regression tests.

#4 bryan-lunt opened 9 years ago
0
Things that should be instance variables are static.

#3 bryan-lunt opened 9 years ago
2
Copious IO inlined in main fuction.

#2 bryan-lunt opened 9 years ago
1
Prediction Scaling

#1 bryan-lunt closed 9 years ago
0