jvivian gene-outlier-detection issues

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.

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issues

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

#80 dauss75 opened 3 years ago
0
installation error

#79 bschilder opened 3 years ago
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Update README.md

#78 jvivian-atreca closed 4 years ago
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Vectorize model & PyMC3 v3.8 compatible (resolves #76, resolves #75)

#77 jvivian closed 4 years ago
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Vectorize model

#76 jvivian closed 4 years ago
2
Make compatible with PyMC3 v3.8

#75 jvivian-atreca closed 4 years ago
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Handle different genes in input and background (resolves #73)

#74 jvivian closed 4 years ago
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Accommodate different gene sets in input and background

#73 jvivian closed 4 years ago
1
Pin PyMC3 to 3.7 to fix backwards-compatibility breaking bug (resolves #71)

#72 jvivian closed 4 years ago
0
Pin PyMC3 to 3.7 for PyPi

#71 jvivian-atreca closed 4 years ago
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Release 1.0

#70 jvivian closed 4 years ago
1
Update plots to handle PyMC3 API change to ArviZ library

#69 jvivian closed 4 years ago
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Expression Metrics and Concordance with Datasets

#68 eyzhao closed 4 years ago
1
Add column for down outliers (resolves #63)

#67 jvivian closed 5 years ago
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Use DataFrame to store fits (resolves #64)

#66 jvivian closed 5 years ago
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Add gelman-rubin statistic to _run_info

#65 jvivian closed 5 years ago
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Change t-fit to return a DataFrame

#64 jvivian closed 5 years ago
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Add 2nd column to pvals.tsv that is the p-value for down-regulated outliers

#63 jvivian closed 5 years ago
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Add tune argument (resolves #59)

#62 jvivian closed 5 years ago
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Refactor library to class (resolves #53)

#61 jvivian closed 5 years ago
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Don't save pkl by default, add switch

#60 jvivian closed 5 years ago
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Expose `tune` step to user

#59 jvivian closed 5 years ago
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propagate --group option to select_k_best_genes call

#58 e-t-k closed 5 years ago
2
Change ANOVA to percent of total genes (resolves #56)

#57 jvivian closed 5 years ago
0
Change number of genes in background selection to 10% instead of hardcoded

#56 jvivian closed 5 years ago
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Use ANOVA for ranking backgrounds (resolves #54)

#55 jvivian closed 5 years ago
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Use ANOVA pairwise distances for ranking background

#54 jvivian closed 5 years ago
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Rewrite library as a class

#53 jvivian closed 5 years ago
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Normalize epsilon by standard deviation (resolves #51)

#52 jvivian closed 5 years ago
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Normalize epsilon by standard deviation

#51 jvivian closed 5 years ago
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Make fancy output plots of genes

#50 jvivian opened 5 years ago
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Move student-T fits to new function

#49 jvivian closed 5 years ago
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Standardize notation

#48 jvivian closed 5 years ago
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Allow unique inputs per sample (resolves #46)

#47 jvivian closed 5 years ago
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Fix toil workflow to allow flexible sample/background/gene-lists

#46 jvivian closed 5 years ago
0
Relax epsilon prior / remove bias term

#45 jvivian closed 5 years ago
0
Make model truly convex by removing bias term (alpha)

#44 jvivian closed 5 years ago
1
Fix _run_info output

#43 jvivian closed 5 years ago
0
Relax epsilon parameter prior

#42 jvivian closed 5 years ago
0
More flexible manifest (resolves #40)

#41 jvivian closed 5 years ago
0
Allow unique options in manifest.txt for toil workflow

#40 jvivian closed 5 years ago
0
Output run information (resolves #38)

#39 jvivian closed 5 years ago
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Save run command to _info

#38 jvivian closed 5 years ago
0
Replace normal with student t (resolves #36)

#37 jvivian closed 5 years ago
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Replace Normal R.V. for expression with StudentT

#36 jvivian closed 5 years ago
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Add iterative output, traceplot params, and move run_info (resolves #27, #33, #34)

#35 jvivian closed 5 years ago
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Move _<files> to subdir _info

#34 jvivian closed 5 years ago
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Add traceplot values to output

#33 jvivian closed 5 years ago
0
Fix outdir and weight cols (resolves #30, resolves #31)

#32 jvivian closed 5 years ago
0
Create output-dir if does not exist in toil workflow

#31 jvivian closed 5 years ago
0