jvivian / gene-outlier-detection

A Bayesian model for identifying gene expression outliers for individual single samples (N-of-1) when compared to a cohort of background datasets.

jvivian/gene-outlier-detection Issues

PermissionError: [Errno 13] Permission denied: 'convert'
Updated 3 years ago
installation error
Updated 3 years ago
Vectorize model
Closed 4 years ago2
Make compatible with PyMC3 v3.8
Closed 4 years ago
Accommodate different gene sets in input and background
Closed 4 years ago1
Pin PyMC3 to 3.7 for PyPi
Closed 4 years ago
Release 1.0
Closed 4 years ago1
Update plots to handle PyMC3 API change to ArviZ library
Closed 4 years ago
Expression Metrics and Concordance with Datasets
Closed 4 years ago1
Add gelman-rubin statistic to _run_info
Closed 5 years ago
Change t-fit to return a DataFrame
Closed 5 years ago
Add 2nd column to pvals.tsv that is the p-value for down-regulated outliers
Closed 5 years ago
Don't save pkl by default, add switch
Closed 5 years ago
Expose `tune` step to user
Closed 5 years ago
propagate --group option to select_k_best_genes call
Closed 5 years ago2
Change number of genes in background selection to 10% instead of hardcoded
Closed 5 years ago
Use ANOVA pairwise distances for ranking background
Closed 5 years ago
Rewrite library as a class
Closed 5 years ago
Normalize epsilon by standard deviation
Closed 5 years ago
Make fancy output plots of genes
Updated 5 years ago
Move student-T fits to new function
Closed 5 years ago
Standardize notation
Closed 5 years ago
Fix toil workflow to allow flexible sample/background/gene-lists
Closed 5 years ago
Make model truly convex by removing bias term (alpha)
Closed 5 years ago1
Fix _run_info output
Closed 5 years ago
Relax epsilon parameter prior
Closed 5 years ago
Allow unique options in manifest.txt for toil workflow
Closed 5 years ago
Save run command to _info
Closed 5 years ago
Replace Normal R.V. for expression with StudentT
Closed 5 years ago
Move _<files> to subdir _info
Closed 5 years ago
Add traceplot values to output
Closed 5 years ago
Create output-dir if does not exist in toil workflow
Closed 5 years ago
Fix terrible columns in `weights.tsv`
Closed 5 years ago
Address coverage holes in tests
Closed 5 years ago
Output pvals/pearsons after each iteration to monitor runs in progress
Closed 5 years ago
Fix theano error during traceplot import
Closed 5 years ago
Fix theano module bug for base_compiledir
Closed 5 years ago
Don't save weights if `n_bg` == 1
Closed 5 years ago
Theano base_compiledir not working as intended
Closed 5 years ago
Employ heuristic when p-values do not converge
Closed 5 years ago1
Once p-values converge, return previous run results
Closed 5 years ago1
Improve CLI and help messages
Closed 5 years ago
Add tests to cover run and iter_run in main.py
Closed 5 years ago
Fix pearson correlation bug
Closed 5 years ago
Update protocol plot
Closed 5 years ago2
Add global runtime
Closed 5 years ago
Add deployment to Travis
Closed 5 years ago
Improve test coverage
Closed 5 years ago
Add iterative model runs to converge num_train parameter
Closed 5 years ago1
Add Tests
Closed 5 years ago