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Revision#31

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miltondp merged 93 commits intomaingreenelab/ccc:mainfrom revisiongreenelab/ccc:revisionCopy head branch name to clipboardJun 18, 2024

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Commits

Commits on Sep 8, 2023

• env.sh: fix path

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• ccc: add initial support for pvalue via permutations

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• ccc: select variable with more partitions for permutation

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• add more unit tests for pvalue computation

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• update ccc version to 0.2.0

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• ccc: add parallelization of permutations (n_jobs_permutations parameter)

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• ccc: rename pvalue-related parameters

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• test_coef: use RandomState object

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• ccc: reorder parameters and improve documentation

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Commits on Sep 11, 2023

• ccc: use get_chunks for pvalue parallelization

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• ccc: set n_chunks_threads_ratio to 2 by default

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• test_coef_pval: disable speed tests on GitHub Actions

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• ccc: do not use ThreadPoolExecutor if n_jobs == 1

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• ccc: optimize code of function get_contingency_matrix

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• add profiling results with the latest implementation

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• ccc: several improvements in terms of parallelization

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• add notebook to check pvalue distribution

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• ccc pvalue: split notebook into generate and plots

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• ccc pvalue: decrease the number of permutations

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• environment/README.md: minor typo

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

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• ccc pvalue: simple notebook rename

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• ccc pvalue: simple notebook rename

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• ccc pvalue: add notebook to compute pvalues using gene pairs

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• ccc pvalue: optimize gene pairs notebook version

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• ccc pvalue: run notebooks to compute pvalues under null

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• jupytext: remove version information

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• ccc pvalue: run notebooks to compute pvalues under null

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• ccc pvalue: update notebook documentation

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• 05_preprocessing: run

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• 10_compute_correlations: simple files rename

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• 10_compute_correlations: use multiple CPU cores with CCC

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

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• 10_compute_correlations: add tqdm for ccc notebook

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• 10_compute_correlations: remove jupytext version info

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• 10_compute_correlations: show N_JOBS for MIC and CCC

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• 10_compute_correlations: run notebooks

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• 15_intersections: run

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• 20_comparison_others: fix directory creation and run notebook

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• 15_intersections: run

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• 20_comparison_others: run notebooks

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• manuscript/time test: run notebook to generate plot

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• manuscript/time test: add assert and run notebook

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

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• manuscript/time test: run notebook to generate plot

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• ccc: improve parallelization of the partitioning step

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• ccc pvalue: run notebooks to compute pvalues under null

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• 10_compute_correlations: run notebooks

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• 20_comparison_others: run

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• run profiling again to ensure new CCC implementation works as expected

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• 99_manuscript/coefs_comp: run notebooks

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

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Commits on Sep 12, 2023

• ccc pvalue: add notebook to sample gene pair categories

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

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Commits on Sep 13, 2023

• ccc: fix problem of random permutations across multiple processes

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• ccc: remove random_state parameter and adjust unit tests

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• ccc pvalue: update gene pair sampling

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• ccc pvalue: increase the number of permutations and compute pearson/spearman p-values

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• ccc pvalue: update gene pair sampling

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• ccc pvalue: update gene pair sampling to 5 gene pairs

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• ccc pvalue: increase the number of permutations and other improvements

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• fix unit test

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• ccc pvalue: run again gene pairs pvalue under null

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• ccc pvalue: compute ccc pvalues on selected gene pair categories

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• ccc pvalue: run again data matrix pvalue under null

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• ccc pvalue: do not sample already selected gene pairs randomly and take a full sample from entire dataset

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Commits on Sep 14, 2023

• ccc pvalue: run sampling

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

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Commits on Sep 18, 2023

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

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• ccc pvalue: add notebook to adjust pvalues

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Commits on Oct 4, 2023

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

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Commits on Oct 10, 2023

• improve notebook documentation

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Commits on Nov 20, 2023

• add notebook to analyze the relationship between UTY and KDM6a

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Commits on Nov 21, 2023

• add notebook to test substructures in data

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Commits on Dec 4, 2023

• figure 1: add p-values in simulated data

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Commits on Dec 6, 2023

• ccc pvalue: minor changes

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• ccc pvalue: add work-in-progress notebook to analyze gene pairs from different categories

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Commits on Jan 3, 2024

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

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• update notebook that analyzes gene pair candidates for figure 3b

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• giant: update with new gene pairs and run notebooks again

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• improve notebooks that generate plots across all GTEx tissues

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• fix wrong abs() method call and run again

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Commits on Jan 4, 2024

• intro/relationships: add simulated categorical datasets

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• setup_data.py: fix URLs to GTEx

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

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Commits on Jan 5, 2024

• supplementary material: add notebook for supplementary file 1

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• supplementary material: add notebook for supplementary file 2

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• supplementary material: add notebook for supplementary file 3

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• update notebook that generates figure 5 (giant)

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Commits on Jan 8, 2024

• add notebook to analyze k_max values

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• k_max analyses: run notebook

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• k_max analyses: add documentation

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• k_max analyses: add notebook to plot results

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