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Claude Skills by HolobiomicsLab
github.com/HolobiomicsLab7,765 skills0 installs8,278 views
- Zero Value Handling In Mass Spectrometry DataUse when after feature detection has produced a feature table with zeroVotes: 0GitHub stars: 15
- Galaxy Workflow4metabolomics Reproducible ProcessingUse when running an LC-MS or GC-MS preprocessing and statistics pipelineVotes: 0GitHub stars: 15
- Metabolomicshub Announcement AuthoringUse when publishing a metabolomics dataset into the MetabolomicsHub indexVotes: 0GitHub stars: 15
- Metabolomicshub Cross Repository Dataset SearchUse when assembling a reanalysis or meta-analysis cohort from publicVotes: 0GitHub stars: 15
- W4m Three Table Format ConformanceUse when moving a feature table between Workflow4Metabolomics tools andVotes: 0GitHub stars: 15
- RouterUse when an agent needs to find and apply a computational-metabolomics / LC-MS-MS skill from this collection, and optionally ground it against the source paper via Perspicacité before acting.Votes: 0GitHub stars: 15
- Asb ContributeUse when an ASB skill proved wrong, stale, missing or wasteful in practice — its steps failed, no skill covered the task, the leaves existed but nothing composed them, or the tool has changed. Turns that friction into a redacted, dedupable report the user approves before anything is filed.Votes: 0GitHub stars: 15
- Asb MetabolomicsUse when starting any task with the ASB Metabolomics skill collection — read this meta-skill first. It explains good practice (search -> apply -> ground), enforces the license-tier acknowledgment for non-open tools, then hands off to the _router skill for actual skill selection.Votes: 0GitHub stars: 15
- Workflow RouterUse when a user has a whole metabolomics analysis GOAL (e.g. "annotate my untargeted LC-MS/MS data", "find biomarkers", "where else has this molecule been seen") rather than a single step — select the right end-to-end composite workflow super-skill, then run its stages, grounding each against its source papers.Votes: 0GitHub stars: 15
- Compound Class Annotation'Use when you want chemical-class-level annotations for untargeted LC-MS/MSVotes: 0GitHub stars: 15
- Fbmn Annotation Propagation'Use when you have untargeted LC-MS/MS MS2 data and want to spread aVotes: 0GitHub stars: 15
- Gcms Deconvolution And Identification'Use when you have GC-MS data (mzML / CDF, typically EI) and want deconvolved,Votes: 0GitHub stars: 15
- Genome Scale Metabolic Flux Modeling'Use when you have a genome-scale constraint-based metabolic model (GEM,Votes: 0GitHub stars: 15
- Gnn Spectral Property Prediction'Use when you want to train or apply a graph neural network over molecularVotes: 0GitHub stars: 15
- In Silico Biotransformation Prediction'Use when you have a parent structure (drug, natural product, xenobiotic)Votes: 0GitHub stars: 15
- Ion Mobility 4d Annotation'Use when you have ion-mobility LC-IMS-MS/MS data (e.g. timsTOF / PASEF)Votes: 0GitHub stars: 15
- Lipidomics Lcms Annotation'Use when you have untargeted lipidomics LC-MS/MS data (mzML) and wantVotes: 0GitHub stars: 15
- Masst Repository Scale Search'Use when you have a spectrum or feature of interest and want to knowVotes: 0GitHub stars: 15
- Ms Imaging Spatial Metabolomics'Use when you have mass-spectrometry imaging data (imzML, e.g. MALDI/DESI)Votes: 0GitHub stars: 15
- Ms2lda Substructure Discovery'Use when you want to discover shared substructures (Mass2Motifs) acrossVotes: 0GitHub stars: 15
- Nmr Metabolomics Profiling'Use when you have NMR metabolomics data (1D/2D spectra or FIDs) andVotes: 0GitHub stars: 15
- Paired Omics Bgc Metabolite Linking'Use when you have paired genomic and metabolomic data from the sameVotes: 0GitHub stars: 15
- Pathway Functional Analysis'Use when you have an LC-MS metabolomics feature list (m/z, optionallyVotes: 0GitHub stars: 15
- Sirius Denovo Structure Elucidation'Use when you have MS/MS for unknown features (a SIRIUS-flavour mgf /Votes: 0GitHub stars: 15
- Spec2vec Ml Embedding Annotation'Use when you want to annotate untargeted MS2 spectra with a machine-learnedVotes: 0GitHub stars: 15
- Stable Isotope Tracing Fluxomics'Use when you have LC-MS data from a stable-isotope (e.g. 13C / 15N)Votes: 0GitHub stars: 15
- Statistics And Biomarker Discovery'Use when you have a metabolomics feature/quant table and want a statisticallyVotes: 0GitHub stars: 15
- Suspect Screening Exposomics'Use when you have untargeted HRMS data and want to screen for a definedVotes: 0GitHub stars: 15
- Targeted Lcms Quantification'Use when you have targeted LC-MS data for a defined panel of analytesVotes: 0GitHub stars: 15
- Untargeted Lcmsms Annotation'Use when you have untargeted LC-MS/MS data (mzML) and want an annotatedVotes: 0GitHub stars: 15
- Adaptive Prior Distribution SelectionUse when after running DESeq() and extracting raw results with results(), when you have log fold change estimates with high variance and wish to improve their precision.Votes: 0GitHub stars: 15
- Adjacency Matrix Sparsity AnalysisUse when immediately after calling squidpy.gr.spatial_neighbors() or similar spatial graph construction methods on an AnnData object. It is essential when validating that the computed spatial graph has been correctly stored in adata.Votes: 0GitHub stars: 15
- Alternative Splicing Event Comparison Across ConditionsUse when you have PSI (percent-spliced-in) matrices calculated independently for two or more biological conditions, each with two or more replicate samples, and you want to identify which alternative splicing events show statistically significant changes in inclusion levels between conditions.Votes: 0GitHub stars: 15
- Alternative Splicing Event ParsingUse when when you have a GTF genome annotation and need to identify all local alternative splicing events (SE, RI, A5/A3, MX, AF/AL) or transcript-level isoform events for a given gene set, prior to quantifying PSI values across samples or performing differential splicing analysis.Votes: 0GitHub stars: 15
- Anndata Object Manipulation And InspectionUse when after executing a Squidpy spatial analysis function (e.g., gr.spatial_neighbors, gr.nhood_enrichment, gr.sepal, im.Votes: 0GitHub stars: 15
- Anndata Object ManipulationUse when you have single-cell RNA-seq count matrices or processed expression data and need to store them alongside cluster assignments (e.g., leiden cluster labels), cell metadata, and computed analysis results (e.Votes: 0GitHub stars: 15
- Anndata Object Structure ValidationUse when after applying Scanpy preprocessing functions (e.g., pp.normalize_total, pp.pca) to a Dask-backed AnnData object, or when performing any operation that could alter matrix dimensions, data types, or backing storage (dense, sparse, or lazy).Votes: 0GitHub stars: 15
- Bayesian Effect Size ModerationUse when after running DESeq2 differential expression analysis and extracting results with raw log fold changes, apply this skill when you observe high variance in effect size estimates across genes—particularly when many genes have small counts, unreliable variance estimates, or when you want.Votes: 0GitHub stars: 15
- Bioconductor Package OperationUse when you have transcript-level quantification files (quant.gz, h5, or similar) from a known upstream quantifier (salmon, kallisto, sailfish, oarfish) and need to import them into R as matrices for differential expression analysis with edgeR, DESeq2, or limma-voom.Votes: 0GitHub stars: 15
- Biological Sequence Read MappingUse when you have raw FASTQ sequencing reads (single-end or paired-end) and a reference transcriptome FASTA file, and you need to determine which transcript(s) each read aligns to in order to quantify transcript abundance. This is the core mapping stage in a salmon quant workflow;Votes: 0GitHub stars: 15
- Boundary Case Read Classification Via Sequence AlignmentUse when when two mapping implementations (or versions of the same mapper) show disagreement on per-read mapping status—e.g., one mapper leaves reads fully unmapped that the other maps, or one maps with high confidence where the other is uncertain.Votes: 0GitHub stars: 15
- Buffer Management And Flush ProtocolsUse when when quantifying or mapping RNA-seq reads with salmon quant using the --writeMappings (-z) flag, or in any streaming output scenario where record count discrepancies appear between reported totals (e.g., NumReads in quant.sf) and file contents (SAM record count).Votes: 0GitHub stars: 15
- C Stream Io DebuggingUse when when a C++ program writes records to an output stream (e.g., SAM alignment file) and the final output file contains fewer records than expected based on upstream counts (e.g., salmon's NumReads total in quant.sf exceeds SAM record count), indicating buffered data loss at stream closure.Votes: 0GitHub stars: 15
- Categorical Annotation Handling In Omics DataUse when you have (1) spatial omics data loaded in AnnData format with a pre-built spatial neighbor graph (from squidpy.gr.spatial_neighbors() or similar), (2) a categorical variable in the AnnData object (e.g., cell type, tissue compartment, annotation stored as .obs or .Votes: 0GitHub stars: 15
- Chain Pruning Threshold OptimizationUse when when comparing mapped read counts between two RNA-seq quantification implementations (e.Votes: 0GitHub stars: 15
- Ci Pipeline Reproducibility VerificationUse when you have cloned a scientific Python project (e.g., scverse/scanpy) and need to verify that your local development environment matches the CI specification before submitting contributions, or when auditing whether the published test suite executes without failures on a fresh checkout.Votes: 0GitHub stars: 15
- Coefficient And Standard Error InterpretationUse when after fitting a linear model to expression data using limma's lmFit function on a design matrix encoding experimental groups, inspect the resulting MArrayLM object to retrieve coefficient estimates (log-fold-changes) and standard errors needed to assess which genes show meaningful.Votes: 0GitHub stars: 15
- Count Data Normalization Rna SeqUse when you have raw read count matrices from RNA-seq quantification (e.g., from featureCounts, HTSeq, Salmon, or kallisto) and need to prepare them for differential expression analysis.Votes: 0GitHub stars: 15
- Count Matrix Format ValidationUse when after constructing a count matrix from transcript quantification files (via tximport, HTSeq, featureCounts, or direct alignment) and before running DESeq() differential expression analysis.Votes: 0GitHub stars: 15
- Dask Array Lazy Evaluation VerificationUse when when applying Scanpy preprocessing functions (e.g., pp.normalize_total, pp.pca) to AnnData objects where the expression matrix X is backed by a dask.array.Array, you need to verify that the operation completed without eagerly loading the full matrix.Votes: 0GitHub stars: 15