Removed presto from DifferentialProximityAnalysis

[ludvigla]

Description

This PR removes the option to use presto for computing Wilcoxon Rank Sum Tests in DifferentialProximityAnalysis. The reason is that presto::wilcoxauc doesn't handle negative values correctly.

Now the default is limma, but falls back to base R wilcox.test if limma is not installed.

Fixes: DAT-124

Type of change

• Bug fix (non-breaking change which fixes an issue).
• New feature (non-breaking change which adds functionality).
• Breaking change (fix or feature that would cause existing functionality to not work as expected).
• This change requires a documentation update.

How Has This Been Tested?

Updated tests for RunDAA and DifferentialProximityAnalysis. These no longer expect the presto backend.

PR checklist:

• My changes generate no new warnings.
• I have added tests that prove my fix is effective or that my feature works.
• I have documented any significant changes to the code in CHANGELOG.md

---

Note

Medium Risk
Changes the statistical engine for Wilcoxon tests in differential proximity (and related) workflows, so p-values can differ from prior releases when presto was used; the fix targets correctness for negative scores.

Overview
Bumps the package to v0.21.0 and documents the change in CHANGELOG.md and the README beta badge.

Wilcoxon rank-sum testing in matrix-based differential proximity analysis (.wilcox_de_test, used by DifferentialProximityAnalysis.Matrix / Seurat "seurat" method) no longer calls presto::wilcoxauc, which mishandled negative proximity values. The path is now limma::rankSumTestWithCorrelation when limma is installed, otherwise stats::wilcox.test per feature, with the install hint updated from presto to limma.

Dependencies: presto and its GitHub Remotes entry are removed from DESCRIPTION. limma remains a Suggests dependency only.

Tests refresh expected p / p_adj values in test-DifferentialProximityAnalysis.R and test-RunDAA.R to match the new test backend (comments about CI expecting presto are dropped).

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[maxkarlsson]

Looks Good!