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HolobiomicsLab

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1. ▌
   Spectral Clustering Density Based · holobiomicslab

   Use when you have computed a sparse pairwise distance matrix from MS/MS spectra (via nearest neighbor indexing) and need to partition spectra into homogeneous clusters—typically when clustering bottom-up proteomics data with the goal of grouping spectra from the same peptide sequence or when you.
   0 installs
2. ▌
   Spectral Data Object Construction · holobiomicslab

   Use when you have a set of centroided .mzML LC-MS files from a targeted metabolomics or lipidomics experiment and need to represent them as a structured object that links raw spectra to sample-level metadata (e.
   0 installs
3. ▌
   Spectral Database Query Execution · holobiomicslab

   Use when when you have an unknown mass spectrum (query spectrum) and need to search it against a reference database of billions of spectra to find matching or structurally related compounds.
   0 installs
4. ▌
   Spectral Denoising Formula Method · holobiomicslab

   Use when you have a noisy MS/MS spectrum and need to identify and remove chemical noise ions (as opposed to electronic noise). You have the precursor compound's SMILES string or molecular formula and its adduct type.
   0 installs
5. ▌
   Spectral Dimensionality Reduction · holobiomicslab

   Use when you have high-resolution tandem MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or searched at scale (millions of spectra).
   0 installs
6. ▌
   Spectral Feature Table Generation · holobiomicslab

   Use when you have raw LC-MS data in mzXML format (or vendor formats convertible via MS-Convert) and need to identify and quantify metabolic features before multi-sample alignment. Use MS1 peak picking for full-scan or DDA data to extract Gaussian and non-Gaussian shaped peaks;
   0 installs
7. ▌
   Spectral Library Entry Generation · holobiomicslab

   Use when you have an experimental or public MS/MS spectrum (e.g., from MassBank in msp format, or a raw centroid-mode chromatogram) and need to create a reusable library entry for a known metabolite.
   0 installs
8. ▌
   Spectral Metadata Standardization · holobiomicslab

   Use when you have mass spectrometry spectra stored across multiple, disparate metabolomics repositories (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA) and need to retrieve them using a single identifier scheme, or you are publishing spectrum figures and need.
   0 installs
9. ▌
   Spectral Molecular Family Linking · holobiomicslab

   Use when when you have pre-processed genomic data (GCFs from AntiSMASH/BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to systematically score and rank putative relationships between biosynthetic gene clusters and their.
   0 installs
10. ▌
    Spectral Peak Annotation Proforma · holobiomicslab

    Use when you have an annotated or raw tandem mass spectrometry spectrum and need to identify which observed peaks correspond to expected peptide fragment ions from a known or predicted peptidoform. Use it before spectrum visualization if you want highlighted, labeled fragment matches;
    0 installs
11. ▌
    Spectrum Peak To Fragment Mapping · holobiomicslab

    Use when when you have a tandem mass spectrum (MS/MS) and a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to identify which observed spectrum peaks correspond to expected b-ion and y-ion fragments, in order to validate peptide identification or annotate spectrum quality.
    0 installs
12. ▌
    Spectrum Relevance Classification · holobiomicslab

    Use when you have a collection of MS/MS spectra from reference standards representing your compounds of interest (e.g., flavonoids, prenylated chalcones) and a set of MS/MS spectra from non-target or other compounds.
    0 installs
13. ▌
    Structural Annotation Integration · holobiomicslab

    Use when you have structural candidates from in silico tools (SIRIUS/CANOPUS) and library spectral matches from GNPS, but need to resolve conflicting or incomplete chemical classifications into a unified consensus.
    0 installs
14. ▌
    Taxonomic Weighting In Annotation · holobiomicslab

    Use when you have a feature table with candidate metabolite annotations (m/z, retention time, chemical identifiers) and MS/MS spectra, and you know the organism or taxon of origin for your samples.
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15. ▌
    Thermo Raw Binary Data Extraction · holobiomicslab

    Use when you have acquired .raw files from a Thermo mass spectrometer (e.g., Q Exactive, Orbitrap) and need to expose their contents—scan numbers, retention times, m/z values, intensities, and precursor information—for downstream nontargeted LCMS feature detection and alignment.
    0 installs
16. ▌
    Topn Acquisition Parameter Tuning · holobiomicslab

    Use when when you have real LC-MS/MS data (mzML format) from an untargeted metabolomics experiment and want to test how variations in TopN DDA parameters affect which precursor ions are selected and fragmented, before deploying the optimized strategy on physical instruments.
    0 installs
17. ▌
    Transformation Product Prediction · holobiomicslab

    Use when after parent chemical suspects have been identified in a non-target screening workflow, use this skill when you need to screen for downstream products formed by chemical or biological transformation.
    0 installs
18. ▌
    Usi String Parsing And Resolution · holobiomicslab

    Use when you have a USI string referencing a spectrum in an online public repository (PRIDE, MassIVE, etc.) and need to load its raw spectral data without downloading the entire dataset file.
    0 installs
19. ▌
    Workflow Output Validation And QA · holobiomicslab

    Use when after executing a Nextflow-based MS-DIAL workflow on .mzML LC-HRMS metabolomics data using Docker or Singularity container backends.
    0 installs
20. ▌
    Xcms Ramclustr Object Integration · holobiomicslab

    Use when you have centroid-mode LC–MS all-ion fragmentation (AIF) data already processed through xcms for feature detection and retention-time correction, and a corresponding RamClustR object that groups co-eluting fragment ions into putative spectral clusters.
    0 installs
21. ▌
    Compound Peak Association Inference · holobiomicslab

    Use when after peak picking on INADEQUATE NMR spectra when you have a set of peak coordinates and intensities and need to determine which peaks belong to the same molecular compound.
    0 installs
22. ▌
    Deep Learning Metabolite Annotation · holobiomicslab

    Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible format) from a water sample, a precursor m/z and retention time of interest, and want to annotate an unknown compound by predicting its molecular formula, structure, and name using deep learning scoring rather than.
    0 installs
23. ▌
    Dom Chemodiversity Characterization · holobiomicslab

    Use when you have a formula-assigned FT-ICR MS dataset (molecular formulas already assigned to individual mass features) and seek to understand the chemodiversity landscape and transformation relationships within DOM.
    0 installs
24. ▌
    Feature Table Consensus Aggregation · holobiomicslab

    Use when you have detected feature tables from multiple LC-IMS-MS/MS samples and need to establish a unified feature catalog in which each row represents a distinct molecular entity observed across one or more samples, with harmonized m/z, drift time, and retention time coordinates.
    0 installs
25. ▌
    Hmdb Metabolite Query And Retrieval · holobiomicslab

    Use when you have identified one or more proton NMR spectral regions-of-interest (ROIs)—defined by lower and upper chemical-shift bounds in ppm—from complex biological samples (serum, saliva, urine, tissue, CSF) and need to generate a ranked list of plausible metabolite identities.
    0 installs
26. ▌
    Interactive Data Exploration Design · holobiomicslab

    Use when you have NMR metabolomics measurements paired with pre-analytical metadata (processing delay times, centrifugation timing, sample type such as plasma vs. serum, cohort identifiers) and need to interactively explore how variation in processing conditions drives changes in metabolic.
    0 installs
27. ▌
    Mass Spectrum Structure Elucidation · holobiomicslab

    Use when you have an experimental tandem mass spectrum (collision-induced dissociation, CID) and a known chemical formula (or narrow set of candidate formulas), and you need to identify the most likely structure(s) by ranking against a large candidate library such as PubChem.
    0 installs
28. ▌
    Metabolite Metadata Column Matching · holobiomicslab

    Use when validating mwTab files deposited to the Metabolomics Workbench and you need to verify that metadata columns match standard naming conventions and contain values in the expected format.
    0 installs
29. ▌
    Metabolite Peak Assignment From Nmr · holobiomicslab

    Use when you have a 1D ¹H NMR spectrum (as chemical shift vs. intensity) and a corresponding peak list (chemical shift values), and you need to identify which metabolites are responsible for each detected peak.
    0 installs
30. ▌
    Nightingale 1h Nmr Data Integration · holobiomicslab

    Use when you have newly assayed 1H-NMR metabolomics data from Nightingale Health (CSV or TSV format) and need to apply one or more published metabolic risk scores (Deelen et al. all-cause mortality, van den Akker MetaboAge, Würtz cardiovascular event risk, etc.).
    0 installs
31. ▌
    Nmr Spectrum To Structure Inference · holobiomicslab

    Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph without manual peak interpretation or exhaustive combinatorial search.
    0 installs
32. ▌
    Pre Analytical Delay Stratification · holobiomicslab

    Use when when you have NMR metabolite measurements paired with documented pre-centrifugation and post-centrifugation delay times, and need to assess how processing delays affect metabolic parameter stability within a plasma or serum sample cohort.
    0 installs
33. ▌
    Spectral Correlation Interpretation · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data (e.g., from plasma or biological samples acquired on a 600 MHz instrument) and need to identify the chemical composition of a prominent but structurally ambiguous peak.
    0 installs
34. ▌
    Spectral Peak Detection And Picking · holobiomicslab

    Use when you have raw INADEQUATE NMR spectra files and need to transition from continuous spectral data to discrete peak coordinates. Use it as the first signal-processing step before clustering peaks into networks or matching against metabolite databases.
    0 installs
35. ▌
    Transformer Based Fragment Assembly · holobiomicslab

    Use when when you have CNN-encoded spectral features (¹H and/or ¹³C NMR) and a set of predicted or candidate molecular fragments, and you need to determine which fragments are present and how they connect to form a valid molecular structure.
    0 installs
36. ▌
    Weighted Loss Function Optimization · holobiomicslab

    Use when when training a dual-encoder architecture (bi-encoder + cross-encoder) on NMR spectral data where independent encoding and joint pair processing produce competing or imbalanced gradient signals.
    0 installs
37. ▌
    Chip Seq Signal Pileup Extension · holobiomicslab

    Use when after duplicate filtering and fragment length prediction (d) in ChIP-Seq analysis, when you need to convert discrete read alignments into continuous coverage signal for comparison against control background.
    0 installs
38. ▌
    Cooler File Loading And Querying · holobiomicslab

    Use when your Hi-C data is stored in cooler format (a binary HDF5-based sparse matrix with associated genomic bins and genomic tracks); you need to programmatically access the contact matrix, bin coordinates, or track data (e.g., eigenvectors, GC content) for further analysis;
    0 installs
39. ▌
    Epigenetic Sample Stratification · holobiomicslab

    Use when after merging methylation call files into a unified methylBase object (covering all samples at common base positions), apply this skill to assess whether biological replicates cluster together, whether case/control or treatment groups separate as expected, and to identify potential sample.
    0 installs
40. ▌
    Genomic Loop Call Interpretation · holobiomicslab

    Use when you have a pre-generated .hic contact map file and need to identify and annotate chromatin loops or topologically associating domains (TADs) at high resolution.
    0 installs
41. ▌
    Local Background Bias Estimation · holobiomicslab

    Use when you have paired ChIP and control BED/BEDPE files and need to account for local sequencing bias before peak calling. Use it specifically when control signal varies across genomic regions at multiple spatial scales (e.
    0 installs
42. ▌
    Poisson Test Statistical Scoring · holobiomicslab

    Use when after generating ChIP pileup and local lambda (background) BEDGRAPH tracks with matched sequencing depth, use this skill to assign statistical significance scores to each genomic region.
    0 installs
43. ▌
    Probe Detection Pvalue Filtering · holobiomicslab

    Use when immediately after loading raw methylation array data (.idat files or beta-valued matrix) from HumanMethylation450 (450k) or EPIC arrays when conducting primary quality control.
    0 installs
44. ▌
    Random Matrix Theory Application · holobiomicslab

    Use when when analyzing normalized DNA methylation beta matrices (450K or EPIC arrays) and you need to identify the true number of latent batch or technical factors present in the data.
    0 installs
45. ▌
    Adduct Mass Difference Matching · holobiomicslab

    Use when you have computed a histogram of pairwise mass differences from MS imaging data and need to (1) identify which observed mass differences correspond to biologically relevant or chemically known adducts, or (2) rank the most frequently observed mass differences to discover dominant adduct.
    0 installs
46. ▌
    Batch Corrected Data Extraction · holobiomicslab

    Use when after batch correction has been applied to metabolomics data using pooled SQC samples, and you need to retrieve the corrected ratios (compound / internal standard) for quality metrics calculation, internal standard recommendation, concentration estimation, or statistical modelling.
    0 installs
47. ▌
    Biclustering For Omics Features · holobiomicslab

    Use when you have a normalized matrix of feature attribution scores (microbes × metabolites) derived from a trained neural network, and you want to partition both microbes and metabolites simultaneously into co-clusters that share similar interaction patterns.
    0 installs
48. ▌
    Biotransformation Rule Encoding · holobiomicslab

    Use when you have untargeted metabolomics data with unknown metabolite structures and need to generate plausible candidate products by systematically applying known enzymatic or chemical transformation rules.
    0 installs
49. ▌
    Chromatographic Method Transfer · holobiomicslab

    Use when you have retention time predictions from a source chromatographic method and need to predict retention times for a target chromatographic method, but have limited calibration data (10–100 molecules) measured on both methods.
    0 installs
50. ▌
    Classifier Prediction Inference · holobiomicslab

    Use when you have a CSV or Excel file containing chemical structure descriptors for one or more molecules, and you want to obtain binary bitter/not-bitter predictions for each molecule using the BitterPredict classifier.
    0 installs
51. ▌
    Confidence Score Interpretation · holobiomicslab

    Use when after executing forward inference on preprocessed mass spectrometry spectra with a deep learning model (e.g., PS²MS), when you have per-spectrum predictions with associated confidence scores or per-class probabilities.
    0 installs
52. ▌
    Cross Language Interface Design · holobiomicslab

    Use when when you have domain-specific functionality (e.g., spectral similarity scoring, peak detection algorithms) implemented in one language (Python) but need to make it callable and composable within an R-based analytical pipeline (Spectra objects);
    0 installs
53. ▌
    Directive Engine Implementation · holobiomicslab

    Use when when you have intermediate JSON data that must be selectively transformed or enriched according to declarative conversion rules—for example, when extracting experimental metadata from tabular spreadsheets, you need to map certain fields to computed or filtered values, apply conditional.
    0 installs
54. ▌
    Distribution Channel Validation · holobiomicslab

    Use when when preparing a software release, testing contribution workflows, or auditing package availability: verify that matchms can be installed and imported successfully from all advertised distribution channels (PyPI and Bioconda) to confirm the package metadata, dependencies, and entry points.
    0 installs
55. ▌
    Fdr Correction Multiple Testing · holobiomicslab

    Use when you have computed empirical p-values from randomized sampling (e.
    0 installs
56. ▌
    Functional Group Classification · holobiomicslab

    Use when you have a set of query chemicals (chemical names or structures) and need to match them against a reference chemical library organized by type or category, with the goal of identifying structural similarity, functional group membership, or categorical assignment.
    0 installs
57. ▌
    Gradient Based Saliency Mapping · holobiomicslab

    Use when you have a trained graph neural network model for CCS prediction and need to identify which molecular structural features drive individual predictions or systematic biases.
    0 installs
58. ▌
    Igzip Header Structure Encoding · holobiomicslab

    Use when when implementing an igzip parser, decoder, or validator that must interpret the custom header format; when debugging igzip file corruption or encoding errors; or when extending pymzML's igzip support to handle new index schemes.
    0 installs
59. ▌
    Ion Mobility Reference Matching · holobiomicslab

    Use when you have raw arrival-time data from TWIM-MS and need to convert it to collision cross section (CCS) values for multi-omic analysis.
    0 installs
60. ▌
    JSON Schema Output Verification · holobiomicslab

    Use when after extracting tabular data into intermediate JSON form or after applying matrix conversion directives (e.
    0 installs
61. ▌
    Lipid Class Coverage Assessment · holobiomicslab

    Use when when you have acquired a CCS reference library (such as DTCCSN2 for U13C labeled lipids) and need to verify that it contains the expected lipid classes, CCS values are physically plausible for ion mobility data, and coverage matches the library's advertised documentation before using it.
    0 installs
62. ▌
    Lipid Class Stratified Analysis · holobiomicslab

    Use when you have IM-MS lipidomics data with measured CCS values, samples spiked with U13C-labeled lipid internal standards (e.
    0 installs
63. ▌
    Lipid Type Category Enumeration · holobiomicslab

    Use when when you have downloaded or cloned a lipidomics library repository (such as LipidMatch) and need to audit the breadth of lipid-type coverage to ensure the library meets minimum requirements for your analysis scope (e.g., ≥60 distinct lipid categories).
    0 installs
64. ▌
    Mass2motif Network Construction · holobiomicslab

    Use when after MS2LDA has inferred a motifset and you need to visualize and export the relationships between discovered Mass2Motifs for post-processing exploration, comparative annotation, or integration with external tools. Use this skill when you have motifset.json or motifset_optimized.
    0 installs
65. ▌
    Molecular Structure Attribution · holobiomicslab

    Use when you have a trained GNN model predicting CCS values from molecular graphs and need to understand which structural features (node and edge attributes) are most influential for specific predictions or across a test set.
    0 installs
66. ▌
    Multi Key Sorting And Filtering · holobiomicslab

    Use when when converting tabular data to JSON via the matrix directive, you need to exclude records that fail domain-specific validation (e.g., only retain records where a 'test' condition evaluates to true) and/or reorder the output list by one or more fields in ascending or descending order.
    0 installs
67. ▌
    Package Repository Verification · holobiomicslab

    Use when releasing a new version of a Python package to public repositories, when verifying that distribution pipelines are functioning after code changes, or when troubleshooting installation failures reported by users across different platforms (Linux, macOS) or architectures (x86_64, aarch64).
    0 installs
68. ▌
    Peak Removal Robustness Testing · holobiomicslab

    Use when when validating a metabolomics pathway analysis method (particularly decomposition-based approaches like PLAGE) against data quality degradation, or when comparing robustness across methods (PLAGE vs. ORA vs. GSEA).
    0 installs
69. ▌
    Post Hoc Model Interpretability · holobiomicslab

    Use when after training a GNN model on molecular structures with continuous targets (e.g., CCS values), when you need to understand which node-level (atom) or edge-level (bond) features contribute most to individual or aggregate predictions.
    0 installs
70. ▌
    Ppm Tolerance Window Adjustment · holobiomicslab

    Use when a mass spectrum calibration procedure initialized with a narrow ppm window (e.g., ±1.0 or ±5.0 ppm) finds fewer than 5 reference m/z matches.
    0 installs
71. ▌
    Prediction Sensitivity Analysis · holobiomicslab

    Use when you have a trained predictor (like BitterPredict) that accepts structured descriptors and want to understand feature importance without retraining.
    0 installs
72. ▌
    Python Automated Test Execution · holobiomicslab

    Use when when contributing code changes to a Python project (fork, feature branch, or pull request) that uses a setup.py-based test suite, before pushing changes to the remote repository or merging into the main branch.
    0 installs
73. ▌
    Rank Order Correlation Analysis · holobiomicslab

    Use when when you have run a pathway ranking method (such as PALS/PLAGE) on clean metabolomics data and wish to assess how sensitive the resulting pathway activity rankings are to realistic data quality issues—specifically Gaussian noise and random peak dropout—which are prevalent in untargeted.
    0 installs
74. ▌
    REST API Contract Documentation · holobiomicslab

    Use when a webservice component (like MAGMa's joblauncher) lacks formal API documentation but the source code is accessible, and downstream consumers (web applications, external services) need to understand available HTTP endpoints, parameter schemas, and response formats without manual.
    0 installs
75. ▌
    Service Health Check Definition · holobiomicslab

    Use when when deploying a multi-service microarchitecture (such as MAGMa's four distinct subprojects: magmaweb, joblauncher, job, and pubchem) via Docker Compose and you need to ensure that service startup order respects true readiness rather than container existence—particularly when services have.
    0 installs
76. ▌
    Spectral Data Format Validation · holobiomicslab

    Use when after converting existing mass spectrometry formats (mzML, vendor formats) into mzPeak using command-line tools or when receiving mzPeak files from external sources.
    0 installs
77. ▌
    Spectrum Subsetting And Merging · holobiomicslab

    Use when when you have a large MsBackend object and need to (1) select a contiguous or non-contiguous range of spectra for focused analysis, or (2) combine spectra from multiple independently-loaded backends (e.
    0 installs
78. ▌
    Structure Organism Pair Binning · holobiomicslab

    Use when when you have loaded a structure-organism pairs table from a natural products database (e.g., LOTUS) and need to answer questions about the distribution of chemical diversity—specifically, how many unique 2D structures appear in exactly 1 organism versus many organisms.
    0 installs
79. ▌
    Binary Spectral Data Extraction · holobiomicslab

    Use when you have parsed imzML XML metadata and loaded the corresponding .ibd binary intensity file, and need to extract specific ion images at one or more target m/z values.
    0 installs
80. ▌
    Bioinformatic Object Conversion · holobiomicslab

    Use when when you have processed Cardinal MSI data (normalized peak intensities, optional SSC segmentation results) and need to transition to Seurat-based workflows for differential expression, pathway analysis, or integration with spatial transcriptomics data.
    0 installs
81. ▌
    Blood Sample Handling Protocols · holobiomicslab

    Use when you are planning a blood sampling campaign and need to verify that lipids or polar metabolites of interest will remain stable through your anticipated sample-processing workflow (specific temperature regimes, delays before/after centrifugation).
    0 installs
82. ▌
    Centrality Metric Normalization · holobiomicslab

    Use when after computing raw betweenness centrality scores for metabolites in a bipartite pathway-metabolite igraph network, when you need to identify metabolites with high topological influence for visualization in ranked plots or when comparing centrality across multiple metabolite subsets or.
    0 installs
83. ▌
    Chromatographic Peak Processing · holobiomicslab

    Use when after peak detection when you have a table of detected peaks with m/z values and retention times from LC/HRMS data, and you observe systematic m/z drift across a batch or population-scale study (n > 500 samples).
    0 installs
84. ▌
    Complementary Score Integration · holobiomicslab

    Use when when you have scored a set of potential gene cluster family (GCF)–molecular feature (MF) links using two or more orthogonal methods (e.
    0 installs
85. ▌
    Compound Identifier Aggregation · holobiomicslab

    Use when you have metabolomics results from multiple studies with compound identifiers in heterogeneous formats (names, InChI strings, SMILES, ChEBI/KEGG/HMDB codes) and need to merge datasets for vote-counting or meta-analysis. Apply this skill before computing consensus measures (e.
    0 installs
86. ▌
    Configuration Schema Validation · holobiomicslab

    Use when when you have generated or edited a LipoCLEAN `options.txt` file using `--print MSD4` or `--print MSD5` and need to verify it is well-formed before running the analysis. Use this skill as a pre-flight check before invoking `--options options.
    0 installs
87. ▌
    Consensus Scoring Meta Analysis · holobiomicslab

    Use when when you have harmonized metabolite data from multiple studies with identifier, fold-change direction, and trend classification columns available, but lack standard deviations or variance estimates needed for quantitative meta-analysis.
    0 installs
88. ▌
    Cytoscape Network Format Export · holobiomicslab

    Use when after constructing or filtering a metabolomic network in MetaMapR (e.g., after applying the unique-edges hierarchy filter to resolve multiple edge types between node pairs), and you need to visualize, share, or further analyze the network using cytoscape.js or compatible tools.
    0 installs
89. ▌
    Data Format Compliance Checking · holobiomicslab

    Use when mSMetaEnhancer fetches metadata from external services (CIR, CTS, PubChem, IDSM, BridgeDb) and must write enriched annotations (SMILES, InChI, CAS numbers, formulas, inchikeys, IUPAC names) into .msp files.
    0 installs
90. ▌
    Differential Expression Ranking · holobiomicslab

    Use when you have completed a two-group or multi-group differential expression analysis with computed logFC values (e.
    0 installs
91. ▌
    Docker Image Layer Optimization · holobiomicslab

    Use when you are building a Docker image for a .NET Framework 4.8 application (like AirdPro) that must run on both Windows native containers and Linux+Wine environments, and you need to reduce build time and image size while maintaining separate targets for GUI, CLI, and development modes.
    0 installs
92. ▌
    Dotnet Assembly Path Resolution · holobiomicslab

    Use when your R package wraps a .NET assembly (e.g., RawFileReader) and you need to (1) report to users or logs which assembly file is actually being used, (2) verify that the assembly exists on disk before attempting to invoke it via system calls, or (3) enable diagnostic output showing the exact.
    0 installs
93. ▌
    Drift Correction Across Batches · holobiomicslab

    Use when your preprocessed metabolomics matrix (log2-scaled, with rows as features and columns as samples) exhibits batch-dependent signal drift or technical variation across multiple analytical runs or instrument sessions.
    0 installs
94. ▌
    Eawag Database Rule Application · holobiomicslab

    Use when when you have small-molecule structures (SMILES or structure format) and need to predict their environmental biotransformation pathways under microbial degradation conditions, particularly when the degradation rules must be drawn from curated, experimentally-validated biodegradation.
    0 installs
95. ▌
    Enrichment Score Interpretation · holobiomicslab

    Use when after differential expression analysis has produced gene lists with p-values and log fold-change values, and after pathway enrichment tools (clusterProfiler or biotranslator) have computed enrichment scores and adjusted p-values.
    0 installs
96. ▌
    Feature Table Format Conversion · holobiomicslab

    Use when you have raw feature tables exported from NPP tools (XCMS, MZmine 2, MS-DIAL, OpenMS, etc.) in their native formats and need to compare their peak detection and alignment performance against a mzRAPP benchmark dataset.
    0 installs
97. ▌
    Fold Change And P Value Ranking · holobiomicslab

    Use when after performing differential abundance testing (via limma or edgeR) on batch-corrected lipid abundance data, use this skill to rank and filter lipids when you need to prioritize results by both effect size and statistical confidence, especially in complex experimental designs with.
    0 installs
98. ▌
    Fold Change Log2 Transformation · holobiomicslab

    Use when when preparing fold-change measurements from multiple metabolomics studies for quantitative meta-analysis via weighted averaging.
    0 installs
99. ▌
    Force Field Minimization Mmff94 · holobiomicslab

    Use when after RDKit generates multiple 3D conformers from ionized molecular structures using distance-geometry embedding, before filtering with ASE-ANI or submitting to quantum calculations.
    0 installs
100. ▌
     Functional Orthology Annotation · holobiomicslab

     Use when after assigning hierarchical KEGG identifiers to a metabolomics count data frame (via assign_hierarchy with identifier='KEGG'), use this skill when you need to link metabolites to their functional roles (KO numbers) and associated genes for downstream functional analysis, pathway.
     0 installs