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Adding MODZ Consensus Signature Operation #53

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merged 11 commits into from
Nov 6, 2019

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@gwaybio gwaybio commented Nov 6, 2019

closes #52

This PR introduces the full functionality to calculate MODZ consensus signatures as introduced in the L1000 Paper. The new modz function implements the moderated z-score transformation as described in https://clue.io/connectopedia/replicate_collapse

This might be helpful to @hkhawar in analyzing drug repurposing cell painting. I think @shntnu was also interested in this at one point.

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Codecov Report

Merging #53 into master will increase coverage by 0.3%.
The diff coverage is 98.75%.

Impacted file tree graph

@@            Coverage Diff            @@
##           master      #53     +/-   ##
=========================================
+ Coverage   96.21%   96.52%   +0.3%     
=========================================
  Files          34       36      +2     
  Lines        1349     1496    +147     
=========================================
+ Hits         1298     1444    +146     
- Misses         51       52      +1
Impacted Files Coverage Δ
pycytominer/tests/test_variance_threshold.py 100% <100%> (ø) ⬆️
pycytominer/tests/test_get_na_columns.py 100% <100%> (ø) ⬆️
pycytominer/cyto_utils/util.py 100% <100%> (ø) ⬆️
pycytominer/cyto_utils/features.py 76.19% <100%> (+1.19%) ⬆️
pycytominer/tests/test_cyto_utils/test_util.py 100% <100%> (ø) ⬆️
...ycytominer/tests/test_cyto_utils/test_consensus.py 100% <100%> (ø)
pycytominer/variance_threshold.py 96.87% <100%> (+0.1%) ⬆️
pycytominer/correlation_threshold.py 100% <100%> (+3.44%) ⬆️
pycytominer/tests/test_correlation_threshold.py 100% <100%> (ø) ⬆️
...ominer/tests/test_cyto_utils/test_feature_infer.py 100% <100%> (ø) ⬆️
... and 5 more

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@gwaybio gwaybio merged commit 3138f3b into cytomining:master Nov 6, 2019
@gwaybio gwaybio deleted the add-modz branch November 6, 2019 18:06
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Add MODZ Aggregation
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