pseudotime-trajectory-viz

Analyze data with `pseudotime-trajectory-viz` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

Quality

37%

Does it follow best practices?

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Securityby

Passed

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tessl review fix ./scientific-skills/Data Analysis/pseudotime-trajectory-viz/SKILL.md

Quality

Content

50%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body contains genuinely useful, actionable technical content (parameters, commands, methods, I/O formats) but is buried under substantial generic process boilerplate and weak file navigation. Pruning the templated sections and explicitly linking the reference file would materially improve it.

Suggestions

Remove or collapse the generic process boilerplate ('Output Requirements', 'Response Template', 'Inputs to Collect', 'Output Contract', 'Lifecycle Status', 'Evaluation Criteria', 'Prerequisites') that adds no skill-specific value.

Replace the generic 'references/' mention with a concrete link to references/runtime_checklist.md and move the bulk Methods/Parameters detail into a reference file to keep SKILL.md a lean overview.

Integrate the py_compile smoke check and a validate-then-proceed feedback loop directly into the Workflow steps so checkpoints are explicit rather than scattered.

Dimension	Reasoning	Score
Conciseness	The ~400-line body is padded with generic boilerplate ('Output Requirements', 'Response Template', 'Inputs to Collect', 'Output Contract', 'Lifecycle Status', 'Evaluation Criteria', 'Security Checklist', 'Prerequisites') and redundant cross-references ('See ## Usage above'), much of it not specific to pseudotime analysis.	2 / 5
Actionability	It provides concrete executable CLI commands, a detailed Parameters table, an Input Format spec, an Output Files tree, and a runnable Python preprocessing example, with only minor gaps (e.g. the odd audit sample string).	4 / 5
Workflow Clarity	A sequenced Workflow section and a py_compile smoke check exist, but validation checkpoints are abstract ('validate the request', 'stop early') and fragmented across sections rather than integrated into the analysis steps.	3 / 5
Progressive Disclosure	Section headers and real bundle files (scripts/main.py, references/runtime_checklist.md) exist, but the reference is only mentioned generically ('references/') rather than linked by filename, and large inline content (Methods, Security Checklist, Parameters) that could be split remains in SKILL.md.	3 / 5
	Total	12 / 20 Passed

Description

25%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is generic and process-oriented rather than capability-oriented, failing to convey the skill's actual single-cell pseudotime purpose or any user-facing trigger. It reads as templated boilerplate that would conflict with many data-analysis skills.

Suggestions

Lead with concrete capabilities, e.g. 'Infer and visualize single-cell developmental trajectories, calculate pseudotime, and overlay gene expression dynamics along lineages.'

Add an explicit trigger clause: 'Use when analyzing single-cell RNA-seq data for differentiation trajectories, pseudotime ordering, or lineage branching.'

Include natural user terms (pseudotime, trajectory, lineage, single-cell, .h5ad) so the skill is distinguishable from generic data-analysis skills.

Dimension	Reasoning	Score
Specificity	The description names only the broad domain ('Analyze data') and lists process qualities ('reproducible workflow, explicit validation, structured outputs') rather than concrete capabilities like pseudotime inference or trajectory visualization.	2 / 5
Completeness	It offers a vague 'what' and entirely lacks a 'when'/'Use when' trigger clause, so neither question is concretely answered.	2 / 5
Trigger Term Quality	It relies on generic terms ('Analyze data', 'structured outputs') and a tool name, omitting the natural phrases a user would say ('pseudotime', 'single-cell trajectory', 'cell differentiation').	2 / 5
Distinctiveness Conflict Risk	'Analyze data with a reproducible workflow' is broad enough to overlap with almost any analytics skill; only the embedded tool name `pseudotime-trajectory-viz` provides any distinguishing signal.	2 / 5
	Total	8 / 20 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
frontmatter_unknown_keys	Unknown frontmatter key(s) found; consider removing or moving to metadata	Warning

	Total	15 / 16 Passed

Repository: aipoch/medical-research-skills
Path: scientific-skills/Data Analysis/pseudotime-trajectory-viz/SKILL.md
Commit: 63c61d3

Reviewed: 9 hours ago

Table of Contents

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