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64 Open 58 Closed
64 Open 58 Closed
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Issues list

Refactor _load_single_patient_variants function enhancement
#251 opened Aug 23, 2017 by jburos
Test new parameters - fail_on_missing_bams, etc enhancement
#250 opened Aug 23, 2017 by jburos
Capture logger output when caching a result enhancement
#248 opened Aug 22, 2017 by jburos
KeyError when predicting neoantigens
#247 opened Aug 22, 2017 by jburos
logging does not respond to user-configured level
#246 opened Aug 22, 2017 by jburos
plot_survival for the whole cohort, not "on" something enhancement
#240 opened Jul 21, 2017 by jburos
Set mhcflurry as the default MHC binding predictor enhancement
#239 opened Jul 21, 2017 by tavinathanson
Explain why predicted neoantigens are NaN when HLA types missing documentation
#238 opened Jul 21, 2017 by jburos
Update README & documentation to match current usage documentation
#234 opened Jul 18, 2017 by jburos
2 tasks
StopIteration error results in cached empty VariantCollection bug
#231 opened Jul 17, 2017 by tavinathanson
Error using median_vaf_purity on a combined-polyphen-snpeff.vcf bug
#228 opened Jul 17, 2017 by jburos
6
Help with creating a cohort
#227 opened Jul 12, 2017 by js2dark
14
Make cohorts more workflow-engine and cloud storage friendly
#226 opened Jul 9, 2017 by armish
1 of 3 tasks
Annoying conflicts between patient-attributes & variables in additional_data
#220 opened Jun 26, 2017 by jburos
Support easy Cohort creation
#218 opened Jun 15, 2017 by tavinathanson
Multi-sample API
#211 opened May 24, 2017 by tavinathanson
4
Optionally Ketrew-ify cache generation?
#209 opened May 19, 2017 by tavinathanson
progress reporting often prints multiple lines bug
#207 opened May 18, 2017 by jburos
2
Cohorts does not work with latest mhctools
#202 opened May 5, 2017 by tavinathanson
2
Add unit test for require_id_str to handle unicode
#200 opened Apr 28, 2017 by jburos
Use reticulate to interface between cohorts (in python) and various analyses (in R)
#198 opened Apr 25, 2017 by jburos
Add support for ordinal benefit categories enhancement
#194 opened Mar 15, 2017 by jburos
1
Fix mhctools API integration
#192 opened Feb 24, 2017 by tavinathanson
Support stratified cohorts, as a way to combine more than one sample of patients
#188 opened Feb 23, 2017 by jburos
1
accomodate sampling weights
#187 opened Feb 23, 2017 by jburos
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