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hammerlab
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cohorts
Utilities for analyzing mutations and neoepitopes in patient cohorts
Apache License 2.0
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progress reporting often prints multiple lines
#207
jburos
opened
7 years ago
2
Add optional show_progress
#206
tavinathanson
closed
7 years ago
6
Update Pageant logic
#205
tavinathanson
closed
7 years ago
9
Drop Python 2 support
#204
tavinathanson
closed
7 years ago
2
TypeError: "load_maf() got an unexpected keyword argument 'encoding'"
#203
jburos
closed
7 years ago
9
Cohorts does not work with latest mhctools
#202
tavinathanson
opened
7 years ago
2
Solve intermittent test failures
#201
tavinathanson
closed
7 years ago
1
Add unit test for `require_id_str` to handle unicode
#200
jburos
opened
7 years ago
0
Update encoding and str handling for Py2/3 compatibility
#199
tavinathanson
closed
7 years ago
2
Use reticulate to interface between cohorts (in python) and various analyses (in R)
#198
jburos
opened
7 years ago
0
Add patient __str__
#197
tavinathanson
closed
7 years ago
2
Fixing filter cache issues
#196
tavinathanson
closed
7 years ago
6
Not identifying filtered-cache-name in python 3
#195
jburos
closed
7 years ago
0
Add support for ordinal `benefit` categories
#194
jburos
opened
7 years ago
1
Don't allow PFS/OS values to be NaN?
#193
tavinathanson
closed
7 years ago
2
Fix mhctools API integration
#192
tavinathanson
opened
7 years ago
0
Add frameshift count function
#191
tavinathanson
closed
7 years ago
0
additional_data should automatically create Patient attributes
#190
tavinathanson
closed
7 years ago
0
Add a median VAF filter function and a filter_fn watermark
#189
tavinathanson
closed
7 years ago
4
Support stratified cohorts, as a way to combine more than one sample of patients
#188
jburos
opened
7 years ago
1
accomodate sampling weights
#187
jburos
opened
7 years ago
0
Refactor and fix functions
#186
tavinathanson
closed
7 years ago
5
Do something with epidisco.py
#185
tavinathanson
opened
7 years ago
1
Minor: old comment
#184
tavinathanson
closed
7 years ago
0
Add watermark for default filter_fn on Cohort initialization
#183
tavinathanson
closed
7 years ago
0
deletion_count is counting all indels
#182
tavinathanson
closed
7 years ago
1
exonic_silent_snv_count is confusing
#181
tavinathanson
closed
7 years ago
1
Add tests for VAF extraction from VCFs, BAMs
#180
tavinathanson
opened
7 years ago
0
Grab VAFs from MAFs
#179
tavinathanson
closed
7 years ago
3
Modify isovar usage from >=3 to >=2 spanning reads
#178
tavinathanson
opened
7 years ago
1
Upgrade isovar to the latest version in cohorts
#177
tavinathanson
closed
7 years ago
2
Add isovar usage tests
#176
tavinathanson
opened
7 years ago
0
Simplify cohorts caching
#175
tavinathanson
opened
7 years ago
2
filter_fn result caching should work for Python 2 and 3
#174
tavinathanson
closed
7 years ago
1
Number of functions is ballooning
#173
tavinathanson
closed
7 years ago
1
Pre-merge exonic counts into develop
#172
jburos
closed
7 years ago
1
Add exonic count functions
#171
jburos
closed
7 years ago
2
Cache sometimes fails if user interrupts writing process
#170
jburos
closed
7 years ago
2
Fix variant stats; cached filtered variants; add exonic counts; add progress bar
#169
jburos
closed
7 years ago
14
Fix variant stats
#168
jburos
closed
7 years ago
0
Support "merged" strelka VCF type
#167
jburos
closed
7 years ago
2
Using only Strelka tier 1 results in divide by zero sometimes
#166
tavinathanson
closed
7 years ago
1
Add more granular variant specification and other minor changes
#165
tavinathanson
closed
7 years ago
7
Random MHC prediction for random cohort
#164
tavinathanson
closed
7 years ago
2
Expressed neoantigens and neoantigens should both use topiary
#163
tavinathanson
opened
7 years ago
0
Harmonize with epidisco
#162
hammer
closed
7 years ago
2
Add variant generation to random_cohorts and more
#161
tavinathanson
closed
7 years ago
1
Add `batch` identifier to cohorts & support estimation of batch effects
#160
jburos
opened
7 years ago
1
Add regplot as a plot_correlation option
#159
tavinathanson
closed
7 years ago
1
Simplify functions with decorators
#158
tavinathanson
closed
7 years ago
2
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