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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

Commits on Sep 8, 2023

  1. env.sh: fix path

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  2. ccc: add initial support for pvalue via permutations

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  3. ccc: select variable with more partitions for permutation

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  4. add more unit tests for pvalue computation

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  5. update ccc version to 0.2.0

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  6. ccc: add parallelization of permutations (n_jobs_permutations parameter)

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  7. ccc: rename pvalue-related parameters

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  8. test_coef: use RandomState object

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  9. ccc: reorder parameters and improve documentation

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Commits on Sep 11, 2023

  1. ccc: use get_chunks for pvalue parallelization

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  2. ccc: set n_chunks_threads_ratio to 2 by default

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  3. test_coef_pval: disable speed tests on GitHub Actions

    @miltondp
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  4. ccc: do not use ThreadPoolExecutor if n_jobs == 1

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  5. ccc: optimize code of function get_contingency_matrix

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  6. add profiling results with the latest implementation

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  7. ccc: several improvements in terms of parallelization 

    * ProcessPoolExecutor is used to parallelize across feature pairs or compute permutations.
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  8. add notebook to check pvalue distribution

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  9. ccc pvalue: split notebook into generate and plots

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  10. ccc pvalue: decrease the number of permutations

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  11. environment/README.md: minor typo

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  12. ccc pvalue: add notebooks for generation and plots on null distribution

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  13. ccc pvalue: simple notebook rename

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  14. ccc pvalue: simple notebook rename

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  15. ccc pvalue: add notebook to compute pvalues using gene pairs

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  16. ccc pvalue: optimize gene pairs notebook version

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  17. ccc pvalue: run notebooks to compute pvalues under null

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  18. jupytext: remove version information

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  19. ccc pvalue: run notebooks to compute pvalues under null

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  20. ccc pvalue: update notebook documentation

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  21. 05_preprocessing: run

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  22. 10_compute_correlations: simple files rename

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  23. 10_compute_correlations: use multiple CPU cores with CCC

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  24. 10_compute_correlations: pearson/spearman, compute only on whole blood

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  25. 10_compute_correlations: add tqdm for ccc notebook

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  26. 10_compute_correlations: remove jupytext version info

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  27. 10_compute_correlations: show N_JOBS for MIC and CCC

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  28. 10_compute_correlations: run notebooks

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  29. 15_intersections: run

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  30. 20_comparison_others: fix directory creation and run notebook

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  31. 15_intersections: run

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  32. 20_comparison_others: run notebooks

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  33. manuscript/time test: run notebook to generate plot

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  34. manuscript/time test: add assert and run notebook

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  35. 20_comparison_others: add time test with 6 CPU cores and run

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  36. manuscript/time test: run notebook to generate plot

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  37. ccc: improve parallelization of the partitioning step

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  38. ccc pvalue: run notebooks to compute pvalues under null

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  39. 10_compute_correlations: run notebooks

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  40. 20_comparison_others: run

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  41. run profiling again to ensure new CCC implementation works as expected

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  42. 99_manuscript/coefs_comp: run notebooks

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  43. 99_manuscript/time_test: generate plot and keep 6 CPU cores

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Commits on Sep 12, 2023

  1. ccc pvalue: add notebook to sample gene pair categories

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  2. ccc pvalue: add notebook to compute CCC/Pearson/Spearman pvalues

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Commits on Sep 13, 2023

  1. ccc: fix problem of random permutations across multiple processes

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  2. ccc: remove random_state parameter and adjust unit tests

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  3. ccc pvalue: update gene pair sampling

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  4. ccc pvalue: increase the number of permutations and compute pearson/s… 

    …pearman p-values
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  5. ccc pvalue: update gene pair sampling

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  6. ccc pvalue: update gene pair sampling to 5 gene pairs

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  7. ccc pvalue: increase the number of permutations and other improvements

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  8. fix unit test

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  9. ccc pvalue: run again gene pairs pvalue under null

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  10. ccc pvalue: compute ccc pvalues on selected gene pair categories

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  11. ccc pvalue: run again data matrix pvalue under null

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  12. ccc pvalue: do not sample already selected gene pairs randomly and ta… 

    …ke a full sample from entire dataset
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Commits on Sep 14, 2023

  1. ccc pvalue: run sampling

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  2. ccc pvalue: run compute of pvalues with 1 million permutations

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Commits on Sep 18, 2023

  1. ccc pvalue: run compute of pvalues with 1 million permutations

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  2. ccc pvalue: add notebook to adjust pvalues

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Commits on Oct 4, 2023

  1. 99_manuscript/time_test: generate plot and keep 3 CPU cores

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Commits on Oct 10, 2023

  1. improve notebook documentation

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Commits on Nov 20, 2023

  1. add notebook to analyze the relationship between UTY and KDM6a

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Commits on Nov 21, 2023

  1. add notebook to test substructures in data

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Commits on Dec 4, 2023

  1. figure 1: add p-values in simulated data

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Commits on Dec 6, 2023

  1. ccc pvalue: minor changes

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  2. ccc pvalue: add work-in-progress notebook to analyze gene pairs from … 

    …different categories
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Commits on Jan 3, 2024

  1. ccc pvalue: finish notebook to analyze gene pairs from Figure 3b

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  2. update notebook that analyzes gene pair candidates for figure 3b 

    * now it considers p-values
* it performs different analyzes by sorting by coefficient and pvalue
* it incorporates information about understudied genes
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  3. giant: update with new gene pairs and run notebooks again

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  4. improve notebooks that generate plots across all GTEx tissues 

    * added pvalue
* added new notebook for kdm6a and ddx3y
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  5. fix wrong abs() method call and run again

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Commits on Jan 4, 2024

  1. intro/relationships: add simulated categorical datasets

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  2. setup_data.py: fix URLs to GTEx

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  3. time test: add table with order of magnitude and remove white background

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Commits on Jan 5, 2024

  1. supplementary material: add notebook for supplementary file 1

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  2. supplementary material: add notebook for supplementary file 2

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  3. supplementary material: add notebook for supplementary file 3

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  4. update notebook that generates figure 5 (giant)

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Commits on Jan 8, 2024

  1. add notebook to analyze k_max values

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  2. k_max analyses: run notebook

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  3. k_max analyses: add documentation

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  4. k_max analyses: add notebook to plot results

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