degenerate-input-filtering
Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant features, zero-variance inputs, all-NaN columns. See nan-safe-correlation for NaN-aware correlation; statistical-analysis for test guidance.
npx skills add BioTender-max/awesome-bio-agent-skills --skill degenerate-input-filtering --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Degenerate Input Filtering Guide ## Overview Degenerate inputs are data points that carry no statistical information: constant-value features, all-NaN columns, single-sequence alignments, empty files, and similar edge cases. When these reach a statistical test or model, the result is meaningless -- a correlation of NaN, a p-value of 1.0, a score of 0.0, or an outright crash. This guide establishes the mandatory practice of detecting and removing such inputs before any analysis, and of reporting every removal so that downstream consumers know the effective sample size. ## Key Concepts ### What Counts as Degenerate A data point is degenerate when it cannot contribute to the statistic being computed. The root cause is always the same: the input lacks the variation or completeness that the method requires. | Type | Example | Why It Fails | |---|---|---| | Constant-value feature | Gene with identical expression across all samples | Variance = 0; correlation, t-test, fold-change are all undefined | | All-NaN feature | Column with no valid observations | Every aggregation returns NaN | | Single-sequence alignment | BLAST result with one sequence | Score = 0.0; no pairwise comparison is
- Overview
- Key Concepts
- What Counts as Degenerate
- Why Silent Failures Are Dangerous
- The Reporting Obligation
- Decision Framework
- Best Practices
- Common Pitfalls
- Workflow
- Reference Implementation
- Sequence Alignment Filtering
- Gene Expression Filtering
- Correlation Pre-filtering
- Expected Output Format
What does the degenerate-input-filtering skill do?
Filter degenerate, uninformative inputs before statistical tests: single-sequence alignments, empty files, constant features, zero-variance inputs, all-NaN columns. See nan-safe-correlation for NaN-aware correlation; statistical-analysis for test guidance.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill degenerate-input-filtering --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.