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Kevin-Haigis-Lab
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speclet
A Bayesian hierarchical model to discover tissue-specific cancer driver genes and synthetic lethal interactions from CRISPR/Cas9 LoF screens.
GNU General Public License v3.0
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Finish up
#196
jhrcook
closed
1 year ago
0
Finishing touches
#195
jhrcook
closed
1 year ago
0
Load data and model objects to FigShare
#194
jhrcook
closed
2 years ago
0
Figures
#193
jhrcook
closed
2 years ago
1
Figures adjustments
#192
jhrcook
closed
2 years ago
1
Expand the analysis to all lineages and sublineages
#191
jhrcook
closed
2 years ago
0
Differences between sexes
#190
jhrcook
closed
2 years ago
0
Merge the various posterior data/cache managers
#189
jhrcook
closed
2 years ago
0
Update model fitting reports
#188
jhrcook
closed
2 years ago
0
Varying chromosome effects nested under cell line
#187
jhrcook
closed
2 years ago
0
Fitting pipeline report should not calculate the log-likelihood
#186
jhrcook
closed
2 years ago
0
Model version and information
#185
jhrcook
closed
2 years ago
0
Refactor cancer gene comutation matrix construction
#184
jhrcook
closed
2 years ago
0
Chromosome varying effects
#183
jhrcook
closed
2 years ago
0
Try a horseshoe prior on the cancer gene comutation variable.
#182
jhrcook
closed
2 years ago
1
Custom PPC plot for fitting pipeline report
#181
jhrcook
closed
2 years ago
1
Add version attribute to bayesian model spec
#180
jhrcook
closed
2 years ago
0
GPU support in the model fitting pipeline
#179
jhrcook
closed
2 years ago
0
Add GPU support for the model fitting pipeline
#178
jhrcook
closed
2 years ago
1
Try running on GPU
#177
jhrcook
closed
2 years ago
2
Simplify the model to help with sampling
#176
jhrcook
closed
2 years ago
1
Experiment with placing sgRNA varying effect under gene
#175
jhrcook
closed
2 years ago
1
Treat cancer genes as standard covariates in the single lineage model
#174
jhrcook
closed
2 years ago
2
Simplify model
#173
jhrcook
closed
2 years ago
3
Single lineage model interface
#172
jhrcook
closed
2 years ago
0
Address CI of pytest suite
#171
jhrcook
closed
2 years ago
0
Single lineage model (and some other additions)
#170
jhrcook
closed
2 years ago
1
Small chores
#169
jhrcook
closed
2 years ago
0
Attempt at modeling the colorectal, pancreas, and esophageal lineages
#168
jhrcook
closed
2 years ago
0
Separate model per cell line lineage
#167
jhrcook
closed
2 years ago
2
Data subset with colorectal, pancreas, and esophagus lineages
#166
jhrcook
closed
2 years ago
0
Refactor SLURM resources and run model-fitting pipeline
#165
jhrcook
closed
2 years ago
0
Try initializing MCMC chains with `advi+adapt_diag`
#164
jhrcook
closed
2 years ago
2
Move SLURM resource requests to model configuration
#163
jhrcook
closed
2 years ago
2
Numpyro PyMC JAX backend
#162
jhrcook
closed
2 years ago
0
Add support for faster PyMC backends
#161
jhrcook
closed
2 years ago
3
Clean
#160
jhrcook
closed
2 years ago
0
Oncogene covariate
#159
jhrcook
closed
2 years ago
0
Posterior predictions on new data
#158
jhrcook
closed
2 years ago
0
Add more pieces to the hierarchical negative binomial model
#157
jhrcook
closed
2 years ago
0
Address failing CI
#156
jhrcook
closed
2 years ago
0
Try upgrading to PyMC v4
#155
jhrcook
closed
2 years ago
4
Fix Theano BLAS warning
#154
jhrcook
closed
2 years ago
0
Better logging system for pystan/httpstan models?
#153
jhrcook
closed
2 years ago
1
Save model configuration with the InferenceData file
#152
jhrcook
closed
2 years ago
0
'gcc' module required by 'slurm-drmaa' results in theano BLAS warning
#151
jhrcook
closed
2 years ago
4
Larger CRC/Bone subsample
#150
jhrcook
closed
2 years ago
0
Negative binomial models
#149
jhrcook
closed
2 years ago
0
Python environment update
#148
jhrcook
closed
2 years ago
0
Refactor modeling system and pipelines for using Stan
#147
jhrcook
closed
2 years ago
0
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