hammerlab cohorts issues

hammerlab / cohorts

Utilities for analyzing mutations and neoepitopes in patient cohorts

Apache License 2.0

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issues

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Allow additional MAF columns

#257 tavinathanson closed 6 years ago
1
Fix effects filtering for splice sites

#256 tavinathanson closed 6 years ago
2
ExonicSpliceSite with Subsitution/etc. alternate_effect is not included in filtering

#255 tavinathanson closed 6 years ago
0
Fix effect priority caching

#254 tavinathanson closed 6 years ago
6
all_effects caches, but does not return, all effects

#253 tavinathanson closed 6 years ago
1
Don't cache after only top-priority effects; post-filter instead

#252 tavinathanson closed 6 years ago
3
Refactor `_load_single_patient_variants` function

#251 jburos opened 6 years ago
0
Test new parameters - fail_on_missing_bams, etc

#250 jburos opened 6 years ago
0
Small fixes to improve estimation of expressed neoantigens

#249 jburos opened 6 years ago
15
Capture logger output when caching a result

#248 jburos opened 6 years ago
0
KeyError when predicting neoantigens

#247 jburos opened 6 years ago
0
logging does not respond to user-configured level

#246 jburos opened 6 years ago
0
Report on but do not error when patient has no RNA data

#245 jburos opened 6 years ago
15
add get-blob method to gcio

#244 jburos closed 6 years ago
1
Add indel effects

#243 jburos opened 6 years ago
7
add `join_on_left` parameter to dataframe_loader

#242 jburos closed 6 years ago
6
Expose gcloud utils

#241 jburos closed 7 years ago
1
plot_survival for the whole cohort, not "on" something

#240 jburos opened 7 years ago
0
Set mhcflurry as the default MHC binding predictor

#239 tavinathanson opened 7 years ago
0
Explain why predicted neoantigens are NaN when HLA types missing

#238 jburos opened 7 years ago
0
Plot surv by strata

#237 jburos closed 6 years ago
8
allow median-vaf-purity with patients having no variants

#236 jburos closed 7 years ago
1
Fix mhcnames to v 0.1.0

#235 jburos closed 7 years ago
2
Update README & documentation to match current usage

#234 jburos opened 7 years ago
0
ImportError: cannot import name 'AlleleParseError'

#233 jburos closed 7 years ago
2
"guess" at variant file format, if not obvious from filename

#232 jburos closed 7 years ago
2
StopIteration error results in cached empty VariantCollection

#231 tavinathanson opened 7 years ago
0
Update warning and associated comment

#230 tavinathanson closed 7 years ago
2
Gcloud batch downloads

#229 jburos closed 7 years ago
3
Error using median_vaf_purity on a combined-polyphen-snpeff.vcf

#228 jburos opened 7 years ago
6
Help with creating a cohort

#227 js2dark opened 7 years ago
14
Make cohorts more workflow-engine and cloud storage friendly

#226 armish opened 7 years ago
0
Feature plot_survival by category (clean branch)

#225 jburos closed 7 years ago
3
Feature - plot survival by category

#224 jburos closed 7 years ago
2
Fix RGBA error with plot_survival

#223 jburos closed 7 years ago
2
Warn on vcf errors

#222 jburos closed 7 years ago
14
Invalid RGBA argument error using `plot_survival`

#221 jburos closed 7 years ago
3
Annoying conflicts between patient-attributes & variables in `additional_data`

#220 jburos opened 7 years ago
0
Google Storage file access add-on for cohorts (a.k.a. minibucket)

#219 armish closed 7 years ago
7
Support easy Cohort creation

#218 tavinathanson opened 7 years ago
0
support plotting survival curves for more than 2 groups

#217 jburos closed 7 years ago
1
add cache_root_dir attribute & behavior

#216 jburos closed 7 years ago
3
refactor caching (more robust API for caching functions)

#215 jburos closed 7 years ago
3
Add `cache_root_dir` attribute

#214 jburos closed 7 years ago
3
small fix to address #212

#213 jburos closed 7 years ago
2
median_vaf_purity() got an unexpected keyword argument 'normalized_per_mb'

#212 jburos closed 7 years ago
1
Multi-sample API

#211 tavinathanson opened 7 years ago
4
Add new PyPi server

#210 tavinathanson closed 7 years ago
2
Optionally Ketrew-ify cache generation?

#209 tavinathanson opened 7 years ago
0
Require Python 3

#208 tavinathanson closed 7 years ago
6