Product & Planning
Product & planning agent skills structure the thinking side of building: specs, PRDs, user stories, roadmaps, and prioritization frameworks. Install one and your AI agent produces planning documents with the same rigor and format every time.
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holobiomicslab Skill Mass Spectrometry Fragmentation Pattern DiscoveryUse when you have preprocessed MS/MS spectral data (in positive or negative ion mode) and seek to discover recurring fragmentation and neutral-loss patterns that characterize molecular substructures across a dataset.
Audited - holobiomicslab Skill Euclidean Distance Computation Approximation
Use when when constructing k-nearest neighbor graphs from spatial coordinates (e.g., microscopy x,y positions or tissue section coordinates) and exact neighbor discovery is computationally prohibitive;
Audited - holobiomicslab Skill Cascade Search Strategy For Peptide Identification
Use when use this strategy when analyzing tandem mass spectrometry data where you expect both unmodified and modified peptide identifications and require high confidence assignments with controlled false discovery rates.
Audited - holobiomicslab Skill Neutral Loss Extraction From Fragmentation Spectra
Use when preparing MS/MS spectra for bag-of-fragments conversion and LDA-based motif discovery. You have raw spectra in supported formats (.mgf, .mzML, or .
Audited - holobiomicslab Skill Missing Value Imputation For Omics
Use when your metabolomic peak table contains missing values (e.g., undetected metabolites below instrument sensitivity or sparse measurements) and you are preparing multi-class or time-course data for statistical analysis, differential profiling, or biomarker discovery.
Audited - holobiomicslab Skill Dot Product Based Spectral Comparison
Use when when searching an unknown MS/MS spectrum against a spectral library and you need to rapidly identify the most relevant candidate library spectra before applying cascade scoring with false discovery rate control.
Audited - holobiomicslab Skill Hotelling T Squared Outlier Detection
Use when after data normalization (Step 7) on the preprocessed feature matrix when you need to identify and flag anomalous samples before statistical testing or biomarker discovery.
Audited - holobiomicslab Skill Mass Spectrometry Data Format Parsing
Use when you have raw MS/MS spectra in one of the supported exchange formats (.mgf, .mzML, or .msp) and need to ingest them into an MS2LDA pipeline for unsupervised motif discovery. This skill is required before any preprocessing, filtering, or ionization-mode-specific handling can occur.
Audited - holobiomicslab Skill Mass Spectrometry File Format Parsing
Use when you have raw MS/MS spectral data in one or more standard mass spectrometry file formats (.mgf, .msp, or .mzML) and need to convert them into a standardized bag-of-fragments representation for unsupervised topic modeling or substructure discovery workflows.
Audited - holobiomicslab Skill Shell Scripting For Program Discovery
Use when a scientific application (such as QCxMS2) requires multiple external programs with specific version constraints and you need to programmatically verify their presence and compatibility before executing calculations.
Audited - holobiomicslab Skill Targeted Feature Extraction From Lcms
Use when you have a curated target list of m/z values, retention times, and identifiers for specific metabolites of interest, and you want to extract only those features from LC-MS data (mzML or netCDF format) rather than performing untargeted feature discovery.
Audited - holobiomicslab Skill Multiclass Biomarker Quality Assessment
Use when you have a multi-class metabolomic peak table with quality control (QC) samples included, and you need to select an optimal preprocessing workflow for downstream biomarker discovery or differential profiling.
Audited - holobiomicslab Skill Spectral Similarity Measure Implementation
Use when you have MSMS spectra from two or more compounds and need to identify which are structurally related. Use this skill when you want to rank spectrum pairs by similarity to discover novel analogs or validate structural assignments in untargeted metabolomics or natural products discovery.
Audited - holobiomicslab Skill Contrastive Learning Encoder Construction
Use when you have mass spectrometry imaging (MSI) data with ion images that need low-dimensional representation learning for downstream tasks like co-localized ion searching or isotope discovery.
Audited - holobiomicslab Skill Bag Of Fragments Representation Construction
Use when after noise filtering and polarity selection of MS/MS spectra (from .mgf, .mzML, or .msp files), when you need to prepare spectra for unsupervised discovery of recurring fragmentation patterns without prior compound identification.
Audited - holobiomicslab Skill Metabolomic Molecular Family Networking Gnps
Use when when you have untargeted LC-MS/MS spectral data from microbial or environmental samples and aim to group related metabolites into molecular families for natural product discovery, especially when integrating with genomic biosynthetic gene cluster (BGC) annotations to link chemistry to.
Audited - holobiomicslab Skill Imaging Mass Spectrometry Ion Identification
Use when you have imaging mass spectrometry data from spatial metabolomics experiments and need to reduce the high-dimensional peak space to a ranked set of marker ions for downstream spatial analysis (e.g., tissue region annotation or biomarker discovery).
Audited - holobiomicslab Skill Bag Of Words Document Representation Generation
Use when you have raw MS/MS spectral data in standard mass spectrometry formats and need to prepare it for unsupervised substructure discovery via topic modeling.
Audited - holobiomicslab Skill Ionization Mode Specific Preprocessing Handling
Use when you have raw MS/MS spectra in supported formats (.mgf, .mzML, or .msp) from mixed ionization modes and need to prepare them for downstream topic modeling (LDA) or motif discovery.
Audited - holobiomicslab Skill Molecular Network Construction For Metabolomics
Use when you have untargeted metabolomics data (e.g., LC-MS/MS spectra) and need to organize compounds by structural relatedness to enable structure discovery for unknown metabolites.
Audited - holobiomicslab Skill Col Mode Augmentation Pipeline Implementation
Use when when you have preprocessed mass spectrometry imaging (MSI) ion images and need to generate augmented image pairs for contrastive learning in co-localized ion discovery tasks.
Audited - holobiomicslab Skill False Discovery Rate Control In Spectral Matching
Use when after performing spectral library matching (whether unmodified or open modification search) and ranking candidate matches by similarity score, apply FDR control when you need to report a curated set of identifications with quantified confidence.
Audited - holobiomicslab Skill Mass Spectrometry Peak Filtering And Noise Reduction
Use when you have raw MS/MS spectra in MGF, mzML, or msp format and need to prepare them for mass2motif discovery or topic modeling.
Audited - holobiomicslab Skill Feature Table Construction For Multivariate Analysis
Use when when you have high-resolution mass-spectrometry (HRMS) breath data in mzML or mzXML format from multiple subjects or conditions and need to prepare a sample-by-feature intensity matrix for downstream statistical comparison, biomarker discovery, or classification tasks.
Audited - holobiomicslab Skill Mass Spectrum Tokenization And Bag Of Fragments Generation
Use when after filtering and cleaning MS/MS spectra (positive/negative ion mode) but before applying Latent Dirichlet Allocation for Mass2Motif discovery.
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diegosouzapw Bundle Idea Osidea-os workflow skill. Use this skill when the user needs Five-phase pipeline (triage → clarify → research → PRD → plan) that turns a raw idea into four linked files: clarifying questions, deep research, a PRD with non-goals and metrics, and a phased execution plan with mermaid user journey and kill criteria and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
54 - diegosouzapw Bundle Codenavi
CodeNavi workflow skill. Use this skill when the user needs Your pathfinder for navigating unknown codebases. Investigates with precision, implements surgically, and never assumes — if it doesn't know, it says so. Maintains a .notebook/ knowledge base that grows across sessions, turning every discovery into lasting intelligence. Summons available skills, MCPs, and docs when the mission demands. Use when fixing bugs, implementing features, refactoring, investigating flows, or any development task in unfamiliar territory. Triggers on "fix this", "implement this", "how does this work", "investigate this flow", "help me with this code". Do NOT use for greenfield scaffolding, CI/CD, or infrastructure provisioning and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
54 - holobiomicslab Skill Spectral Noise Filtering And Quality Control
Use when you have raw MS/MS spectra in multiple formats (.mgf, .msp, .mzML) that contain background noise, instrument artifacts, or low-abundance fragments that would degrade downstream LDA motif discovery.
Audited - holobiomicslab Skill Decoy Database Generation For Metabolomics
Use when performing large-scale untargeted metabolomics annotation where you need to estimate the false discovery rate of metabolite identifications.
Audited - holobiomicslab Skill False Discovery Rate Estimation Untargeted
Use when performing untargeted metabolomics annotation (i.e., matching observed spectra to a compound database without a pre-defined target list) and you need to assign statistical significance or confidence to candidate metabolite identifications.
Audited - holobiomicslab Skill Statistical Significance Filtering Q Value
Use when after performing univariate statistical tests (e.g., ANOVA, t-tests) across sample classes in a normalized metabolomic feature table, you need to control false discovery rate and select a high-confidence subset of significantly differentiated metabolites for downstream analysis (e.
Audited - diegosouzapw Bundle Nx Generate
Run Nx Generator workflow skill. Use this skill when the user needs Generate code using Nx generators — scaffold projects, libraries, features, or run workspace-specific generators with proper discovery, validation, and verification. Use when user says "create a new library", "scaffold a component", "generate code with Nx", "run a generator", "nx generate", or any code scaffolding task in a monorepo. Prefers local workspace-plugin generators over external plugins. Do NOT use for running build/test/lint tasks (use nx-run-tasks) or workspace configuration (use nx-workspace) and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
54 - diegosouzapw Bundle Vexor CLI V2
Vexor CLI Skill workflow skill. Use this skill when the user needs Semantic file discovery via vexor. Use whenever locating where something is implemented/loaded/defined in a medium or large repo, or when the file location is unclear. Prefer this over manual browsing and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
54 - diegosouzapw Bundle Exa Search V2
exa-search workflow skill. Use this skill when the user needs Semantic search, similar content discovery, and structured research using Exa API. Use when you need semantic/embeddings-based search, finding similar content, or searching by category (company, people, research papers, etc.) and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
54 - diegosouzapw Bundle Vexor CLI
Vexor CLI Skill workflow skill. Use this skill when the user needs Semantic file discovery via vexor. Use whenever locating where something is implemented/loaded/defined in a medium or large repo, or when the file location is unclear. Prefer this over manual browsing and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
54 - diegosouzapw Bundle Create Rfc
RFC Creator workflow skill. Use this skill when the user needs Creates structured Request for Comments (RFC) documents for proposing and deciding on significant changes. Use when the user says "write an RFC", "create a proposal", "I need to propose a change", "draft an RFC", "document a decision", or needs stakeholder alignment before making a major technical or process decision. Do NOT use for TDDs/implementation docs (use technical-design-doc-creator instead), README files, or general documentation and the operator should preserve the upstream workflow, copied support files, and provenance before merging or handing off.
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Frequently asked questions
What are Product & Planning agent skills?
Product & planning agent skills structure the thinking side of building: specs, PRDs, user stories, roadmaps, and prioritization frameworks. Install one and your AI agent produces planning documents with the same rigor and format every time.
Which Product & Planning skills are most installed?
Popular Product & Planning skills on SkillMD right now include mass-spectrometry-fragmentation-pattern-discovery, euclidean-distance-computation-approximation, cascade-search-strategy-for-peptide-identification. Rankings shift as installs change; sort this page by "Most installs" for the live list.
Do Product & Planning skills work with Claude Code and Cursor?
Yes. Every skill here ships as a SKILL.md file, an open format that works in Claude Code, Claude.ai, Cursor, Codex, Windsurf, and 60+ other agents. Install one with npx skillmds@latest add <owner>/<name>, or copy the file into your agent's skills directory.