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Claude Skills by HolobiomicsLab
github.com/HolobiomicsLab4,372 skills13 installs12,718 views
- ISSUE TEMPLATE<!-- Use this when YOU are the author of the tool (or method/paper) a skill grounds on, and you want to contribute that skill AND be credited as a co-author. Keep it short: tell us the tool/paper, what the skill does, and who you are. A maintainer runs the `claim-skill` command, which normalizes/matches/grounds the skill (the propose-skill flow), writes you into the staged skill's `contributors` as `role: author`, and stages a reviewable PR with `Co-authored-by:` you. A maintainer makes the f...Votes: 0GitHub stars: 16
- ISSUE TEMPLATE<!-- Keep this short. A meta-skill (super-skill) does NOT re-implement a procedure — it SEQUENCES existing sub-skills into a canonical end-to-end pipeline (e.g. "molecular networking": feature detection/alignment → spectral similarity/networking → annotation/propagation → visualization). Tell us WHAT pipeline it captures, WHICH sub-skills/tools it should orchestrate, and WHY it's worth shipping as a super-skill. The `synthesize-meta-skill` command does the synthesis, grounding, and normalizat...Votes: 0GitHub stars: 16
- ISSUE TEMPLATE<!-- Keep this short. Tell us WHAT the skill does, WHY it's worth adding, and give a LINK to the skill (or paste its SKILL.md). The `propose-skill` command does the matching, grounding, and normalization, and stages a reviewable PR. A maintainer makes the final merge decision — you cannot self-merge. See governance/COMMUNITY_SKILLS.md for how community skills are curated. --> **What does the skill do?** <!-- one line, e.g. "Use when aligning RT across batches with method X" --> **Why it matte...Votes: 0GitHub stars: 16
- ISSUE TEMPLATE> 🧩 **What this is:** a super-skill is a *composite workflow* — an ordered DAG of > **existing leaf skills** for an end-to-end task (e.g. `mzML → annotation`). It is > generated from a short **skeleton** (stages + goals + preferred leaf skills) by > the ASB factory, not hand-written. It reuses leaves; it does not add new ones. > To add a *new tool/paper*, file a [Propose a paper](./3-propose-paper.md) instead.Votes: 0GitHub stars: 16
- 2d Nmr Pulse Sequence ImplementationUse when when you need to generate 2D metabolomic NMR spectra (COSY forVotes: 0GitHub stars: 16
- 2d Tic PreprocessingUse when when you have raw GCxGC-MS data imported from NetCDF into aVotes: 0GitHub stars: 16
- 4d Lcimmsms Feature ExtractionUse when you have raw LC-IM-MS/MS data files from sterol lipid analysisVotes: 0GitHub stars: 16
- Ablation Study Design And InterpretationUse when when you have a neural network or machine learning model withVotes: 0GitHub stars: 16
- Abstract Base Class ImplementationUse when when building a visualization library that must support multipleVotes: 0GitHub stars: 16
- Abstract Syntax Tree ConstructionUse when you have a tokenized sequence of domain-specific language tokensVotes: 0GitHub stars: 16
- Abstract Syntax Tree DesignUse when when you have a domain-specific query language (such as MassQLVotes: 0GitHub stars: 16
- Abundance Normalization And Summary StatisticsUse when after peaks have been assigned to heteroatom classes (e.g.,Votes: 0GitHub stars: 16
- Accuracy Metric ComputationUse when after running inference on a trained structure prediction modelVotes: 0GitHub stars: 16
- Accurate Mass Database SearchUse when after peak detection and MS1 feature extraction from FIA-MS,Votes: 0GitHub stars: 16
- Accurate Mass Metabolite Search Against HmdbUse when after MS1 feature detection and spectra merging in an untargetedVotes: 0GitHub stars: 16
- Acquisition Method Overlap AnalysisUse when you have acquired the same sample(s) using multiple LC-MS, LC-IMS-MS,Votes: 0GitHub stars: 16
- Acquisition Mode Enumeration And ValidationUse when adopting a mass spectrometry-based analysis tool (e.Votes: 0GitHub stars: 16
- Activity Score Robustness AssessmentUse when after computing PLAGE-derived activity scores for pathways orVotes: 0GitHub stars: 16
- Adduct And Fragment Neutral Mass CalculationUse when you have an LC-MS peak-intensity matrix with observed m/z valuesVotes: 0GitHub stars: 16
- Adduct Annotation Against Reference LibraryUse when after computing a histogram of all pairwise mass differencesVotes: 0GitHub stars: 16
- Adduct Assignment Accuracy AssessmentUse when you have a trained formula ranking model (such as MIST-CF) andVotes: 0GitHub stars: 16
- Adduct Based Feature ConsolidationUse when after accurate mass searching has assigned multiple detectedVotes: 0GitHub stars: 16
- Adduct Form Prediction And Mass CalculationUse when you have a characterized lipid species (with defined class andVotes: 0GitHub stars: 16
- Adduct Formation Prediction For MetabolitesUse when when you have unidentified LC/MS features (m/z, retention time,Votes: 0GitHub stars: 16
- Adduct Fragment Formula InterpretationUse when after temporal correlation has identified candidate featureVotes: 0GitHub stars: 16
- Adduct Fragment Table ConstructionUse when when initializing an mWISE annotation pipeline with a new orVotes: 0GitHub stars: 16
- Adduct Ion Mass CalculationUse when when you have derivatized metabolite structures (SMILES or molVotes: 0GitHub stars: 16
- Adduct Ion Parent Ion Pairing AnalysisUse when when you have binned mass spectrometry imaging peaks and wantVotes: 0GitHub stars: 16
- Adduct Ion Prediction And Filtering'Use when when annotating m/z features against a metabolite databaseVotes: 0GitHub stars: 16
- Adduct Ionmode Consistency CheckingUse when parsing, standardizing, or filtering MS spectra from mixed orVotes: 0GitHub stars: 16
- Adduct Mass Adjustment CalculationUse when you have a set of in silico-predicted compounds (with SMILESVotes: 0GitHub stars: 16
- Adduct Mass Calculation And MatchingUse when when you have a list of target molecules with known molecularVotes: 0GitHub stars: 16
- Adduct Mass Calculation From SmilesUse when when you have a metabolite SMILES structure and need to predictVotes: 0GitHub stars: 16
- Adduct Mass Difference MatchingUse when you have computed a histogram of pairwise mass differences fromVotes: 0GitHub stars: 16
- Adduct Mass Difference RankingUse when you have computed a histogram of mass differences from all pairwiseVotes: 0GitHub stars: 16
- Adduct Mass Matching And ClusteringUse when after identifying statistically significant LC-MS features (e.g.Votes: 0GitHub stars: 16
- Adduct Mass Offset AssignmentUse when when you have an LC-MS feature table with m/z and retentionVotes: 0GitHub stars: 16
- Adduct Mass Offset ParameterizationUse when when processing LC-MS metabolomics feature tables where adductVotes: 0GitHub stars: 16
- Adduct Mass Shift CalculationUse when when you have a list of observed m/z values from LC/MS featureVotes: 0GitHub stars: 16
- Adduct Regex Pattern MatchingUse when ingesting mass spectrometry spectra from heterogeneous databasesVotes: 0GitHub stars: 16
- Adduct Signature Identification Mass SpectrometryUse when you have statistically significant LC-MS features (e.g., filteredVotes: 0GitHub stars: 16
- Adduct Specific Model Fine TuningUse when when you have access to annotated MS/MS spectra from a specificVotes: 0GitHub stars: 16
- Adduct Type Assignment Positive ModeUse when you have an unknown MS/MS spectrum with a measured precursorVotes: 0GitHub stars: 16
- Aif Spectrum Fragment Database MatchingUse when you have a feature table from untargeted LC–MS all-ion fragmentationVotes: 0GitHub stars: 16
- Aird Format Conversion And ValidationUse when you have vendor mass spectrometry raw files (e.g., .raw, .d,Votes: 0GitHub stars: 16
- Algorithm Interface AbstractionUse when you have multiple independent peak-picking algorithms availableVotes: 0GitHub stars: 16
- Algorithm Parameter Comparison AnalysisUse when when you need to evaluate how a specific algorithm parameterVotes: 0GitHub stars: 16
- Algorithm Performance BenchmarkingUse when you have refactored or reimplemented a core computational methodVotes: 0GitHub stars: 16
- Aligned Feature Matrix ConstructionUse when when you have extracted feature tables from multiple breathVotes: 0GitHub stars: 16
- Aligned Feature Table ManipulationUse when after multi-sample alignment has been completed in JPA (PartVotes: 0GitHub stars: 16