jvivian/gene-outlier-detection

Issues

• PermissionError: [Errno 13] Permission denied: 'convert'

  #80 opened 3 years ago by dauss75
  0

• installation error

  #79 opened 3 years ago by bschilder
  0

• Release 1.0

  #70 opened 4 years ago by jvivian
  1

• Make compatible with PyMC3 v3.8

  #75 opened 4 years ago by jvivian-atreca
  0

• Vectorize model

  #76 opened 4 years ago by jvivian
  2

• Accommodate different gene sets in input and background

  #73 opened 4 years ago by jvivian
  1

• Update plots to handle PyMC3 API change to ArviZ library

  #69 opened 5 years ago by jvivian
  0

• Pin PyMC3 to 3.7 for PyPi

  #71 opened 5 years ago by jvivian-atreca
  0

• Expression Metrics and Concordance with Datasets

  #68 opened 5 years ago by eyzhao
  1

• Add 2nd column to pvals.tsv that is the p-value for down-regulated outliers

  #63 opened 5 years ago by jvivian
  0

• Add gelman-rubin statistic to _run_info

  #65 opened 5 years ago by jvivian
  0

• Change t-fit to return a DataFrame

  #64 opened 5 years ago by jvivian
  0

• propagate --group option to select_k_best_genes call

  #58 opened 5 years ago by e-t-k
  2

• Expose `tune` step to user

  #59 opened 5 years ago by jvivian
  0

• Don't save pkl by default, add switch

  #60 opened 5 years ago by jvivian
  0

• Employ heuristic when p-values do not converge

  #20 opened 5 years ago by jvivian
  1

• Rewrite library as a class

  #53 opened 5 years ago by jvivian
  0

• Change number of genes in background selection to 10% instead of hardcoded

  #56 opened 5 years ago by jvivian
  0

• Use ANOVA pairwise distances for ranking background

  #54 opened 5 years ago by jvivian
  0

• Normalize epsilon by standard deviation

  #51 opened 5 years ago by jvivian
  0

• Move student-T fits to new function

  #49 opened 5 years ago by jvivian
  0

• Standardize notation

  #48 opened 5 years ago by jvivian
  0

• Make fancy output plots of genes

  #50 opened 5 years ago by jvivian
  0

• Make model truly convex by removing bias term (alpha)

  #44 opened 5 years ago by jvivian
  1

• Fix toil workflow to allow flexible sample/background/gene-lists

  #46 opened 5 years ago by jvivian
  0

• Relax epsilon parameter prior

  #42 opened 5 years ago by jvivian
  0

• Fix _run_info output

  #43 opened 5 years ago by jvivian
  0

• Allow unique options in manifest.txt for toil workflow

  #40 opened 5 years ago by jvivian
  0

• Once p-values converge, return previous run results

  #19 opened 5 years ago by jvivian
  1

• Save run command to _info

  #38 opened 5 years ago by jvivian
  0

• Replace Normal R.V. for expression with StudentT

  #36 opened 5 years ago by jvivian
  0

• Output pvals/pearsons after each iteration to monitor runs in progress

  #27 opened 5 years ago by jvivian
  0

• Add traceplot values to output

  #33 opened 5 years ago by jvivian
  0

• Move _<files> to subdir _info

  #34 opened 5 years ago by jvivian
  0

• Fix terrible columns in `weights.tsv`

  #30 opened 5 years ago by jvivian
  0

• Create output-dir if does not exist in toil workflow

  #31 opened 5 years ago by jvivian
  0

• Address coverage holes in tests

  #29 opened 5 years ago by jvivian
  0

• Fix theano error during traceplot import

  #26 opened 5 years ago by jvivian
  0

• Don't save weights if `n_bg` == 1

  #23 opened 5 years ago by jvivian
  0

• Fix theano module bug for base_compiledir

  #24 opened 5 years ago by jvivian
  0

• Theano base_compiledir not working as intended

  #21 opened 5 years ago by jvivian
  0

• Improve CLI and help messages

  #17 opened 5 years ago by jvivian
  0

• Add tests to cover run and iter_run in main.py

  #15 opened 5 years ago by jvivian
  0

• Update protocol plot

  #12 opened 5 years ago by jvivian
  2

• Fix pearson correlation bug

  #13 opened 5 years ago by jvivian
  0

• Add global runtime

  #10 opened 5 years ago by jvivian
  0

• Add deployment to Travis

  #8 opened 5 years ago by jvivian
  0

• Add iterative model runs to converge num_train parameter

  #3 opened 5 years ago by jvivian
  1

• Improve test coverage

  #5 opened 5 years ago by jvivian
  0

• Add Tests

  #2 opened 5 years ago by jvivian
  0