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Revision #31

Merged
merged 93 commits into from
Jun 18, 2024
Merged

Revision #31

merged 93 commits into from
Jun 18, 2024

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miltondp
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@miltondp miltondp commented Jan 3, 2024

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@miltondp
env.sh: fix path
59ee1f2
@miltondp
ccc: add initial support for pvalue via permutations
92bdb04
@miltondp
ccc: select variable with more partitions for permutation
7a9124b
@miltondp
add more unit tests for pvalue computation
3a08266
@miltondp
update ccc version to 0.2.0
c099427
@miltondp
ccc: add parallelization of permutations (n_jobs_permutations parameter)
3e4edf1
@miltondp
ccc: rename pvalue-related parameters
1c9f30f
@miltondp
test_coef: use RandomState object
b2faf95
@miltondp
ccc: reorder parameters and improve documentation
4aeb8ba
@miltondp
ccc: use get_chunks for pvalue parallelization
a6a186f
@miltondp
ccc: set n_chunks_threads_ratio to 2 by default
481364c
@miltondp
test_coef_pval: disable speed tests on GitHub Actions
1c2a6bf
@miltondp
ccc: do not use ThreadPoolExecutor if n_jobs == 1
617075b
@miltondp
ccc: optimize code of function get_contingency_matrix
976e555
@miltondp
add profiling results with the latest implementation
5e18650
@miltondp
ccc: several improvements in terms of parallelization
bf0d17a 
* ProcessPoolExecutor is used to parallelize across feature pairs or compute permutations.
@miltondp
add notebook to check pvalue distribution
3c1c032
@miltondp
ccc pvalue: split notebook into generate and plots
f57160c
@miltondp
ccc pvalue: decrease the number of permutations
2dc4865
@miltondp
environment/README.md: minor typo
56bd6c3
@miltondp
ccc pvalue: add notebooks for generation and plots on null distribution
42e509a
@miltondp
ccc pvalue: simple notebook rename
4891122
@miltondp
ccc pvalue: simple notebook rename
7b202ef
@miltondp
ccc pvalue: add notebook to compute pvalues using gene pairs
a7aae4c
@miltondp
ccc pvalue: optimize gene pairs notebook version
60ccf10
@miltondp
ccc pvalue: run notebooks to compute pvalues under null
dc53ac4
@miltondp
jupytext: remove version information
149a1ab
@miltondp
ccc pvalue: run notebooks to compute pvalues under null
47e0059
@miltondp
ccc pvalue: update notebook documentation
3a82a64
@miltondp
05_preprocessing: run
3c8d7f4
@miltondp
ccc pvalue: run compute of pvalues with 1 million permutations
dd328cc
@miltondp
ccc pvalue: add notebook to adjust pvalues
f96173f
@miltondp
99_manuscript/time_test: generate plot and keep 3 CPU cores
d477639
@miltondp
improve notebook documentation
ea19456
@miltondp
add notebook to analyze the relationship between UTY and KDM6a
fe25b68
@miltondp
add notebook to test substructures in data
b68a0dc
@miltondp
figure 1: add p-values in simulated data
a1ccad0
@miltondp
ccc pvalue: minor changes
09e032f
@miltondp
ccc pvalue: add work-in-progress notebook to analyze gene pairs from …
8e1f94f 
…different categories
@miltondp
ccc pvalue: finish notebook to analyze gene pairs from Figure 3b
123b5e7
@miltondp
update notebook that analyzes gene pair candidates for figure 3b
09e83f8 
* now it considers p-values
* it performs different analyzes by sorting by coefficient and pvalue
* it incorporates information about understudied genes
@miltondp
giant: update with new gene pairs and run notebooks again
1c16d6f
@miltondp
improve notebooks that generate plots across all GTEx tissues
0df3097 
* added pvalue
* added new notebook for kdm6a and ddx3y
@miltondp
fix wrong abs() method call and run again
9b670d0
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codecov-commenter commented Jan 4, 2024 •
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Codecov Report

Attention: 16 lines in your changes are missing coverage. Please review.

Comparison is base (050cae8) 99.11% compared to head (be60eb6) 96.86%.

Files Patch % Lines
libs/ccc/coef/impl.py 86.91% 14 Missing ⚠️
libs/ccc/utils/utility_functions.py 77.77% 2 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #31      +/-   ##
==========================================
- Coverage   99.11%   96.86%   -2.25%     
==========================================
  Files          15       15              
  Lines         564      638      +74     
==========================================
+ Hits          559      618      +59     
- Misses          5       20      +15

☔ View full report in Codecov by Sentry.
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@miltondp miltondp marked this pull request as ready for review June 18, 2024 19:51
@miltondp miltondp merged commit c08fd4f into main Jun 18, 2024
8 of 9 checks passed
@miltondp miltondp deleted the revision branch June 18, 2024 19:52
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@miltondp @codecov-commenter