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HolobiomicsLab

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1. ▌
   Scan Index Parsing And Filtering · holobiomicslab

   Use when you have a Thermo Orbitrap .raw file and need to (1) verify that a targeted acquisition method (e.g., PRM) maintains consistent scan spacing across all cycles; (2) extract only scans matching a specific precursor ion and fragmentation method;
   0 installs
2. ▌
   Score Distribution Visualization · holobiomicslab

   Use when after computing link scores (e.g., strain correlation, IOKR, or combined scores) across GCF-MF pairs, use this skill to assess whether scores achieve sufficient separation between validated links and the background population.
   0 installs
3. ▌
   Signal Apodization Configuration · holobiomicslab

   Use when when processing raw Bruker Solarix transient files (.d format) destined for FT-MS analysis, especially for ESI-negative or low-abundance natural organic matter samples where baseline noise and side-lobe artifacts around intense peaks degrade peak picking and formula assignment accuracy.
   0 installs
4. ▌
   Small Molecule Compound Indexing · holobiomicslab

   Use when when you have retention order predictions from multiple ensemble members (e.g., ROASMI_1 through ROASMI_5) for a set of candidate compounds and need to assign a per-compound uncertainty score that reflects how consistently the ensemble members rank that compound relative to others.
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5. ▌
   Smoothing Spline Basis Selection · holobiomicslab

   Use when you have a set of anchor feature pairs (m/z and retention time values) from two disparately-acquired LC-MS datasets and need to fit a smooth, nonlinear RT correction spline.
   0 installs
6. ▌
   Spectral Data Import And Parsing · holobiomicslab

   Use when you have raw mass spectrometry data in one or more supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, or JSON) and need to convert it into a standardized in-memory representation that can be processed, validated, and compared using matchms.
   0 installs
7. ▌
   Spectral Feature Standardization · holobiomicslab

   Use when after peak-picking stage completes on centroided mzML or netCDF raw LC-MS data via any of the three wrapped algorithms (Centwave, FeatureFinderMetabo, ADAP), when you need to pass the detected features to downstream SLAW stages (alignment, isotope/adduct grouping, gap-filling, MS2.
   0 installs
8. ▌
   Spectral Fragment Ion Annotation · holobiomicslab

   Use when you have an MS/MS spectrum (m/z and intensity arrays) and a known or hypothesized peptide sequence (optionally with post-translational modifications in ProForma 2.
   0 installs
9. ▌
   Spectral Intensity Normalisation · holobiomicslab

   Use when processing raw MS/MS spectra (in MGF, mzML, mzXML, JSON, or MSP format) prior to MS2Query library matching or MS2Deepscore embedding calculation.
   0 installs
10. ▌
    Spectral Intensity Normalization · holobiomicslab

    Use when after removing precursor and noise peaks from an MsmsSpectrum object when the spectrum contains peaks with highly variable intensities (e.g., one or two dominant peaks with many weaker fragments).
    0 installs
11. ▌
    Spectral Peak Embedding Encoding · holobiomicslab

    Use when when you have variable-length MS/MS peak lists (m/z and intensity arrays) that must be fed into a transformer-based model for spectra analysis, and you need deterministic, normalized embeddings that preserve peak frequency information across multiple scales.
    0 installs
12. ▌
    Spectrum Annotation Augmentation · holobiomicslab

    Use when you have a TCN-predicted training set of MS/MS spectra with formula annotations and need to prepare it for Siamese rescore model training.
    0 installs
13. ▌
    Synthetic Lcmsms Data Generation · holobiomicslab

    Use when you need to create defined LC-MS/MS datasets with known molecular composition and fragmentation patterns for algorithm validation, method development, or evaluation of analytical challenges (e.g., co-elution prediction).
    0 installs
14. ▌
    System Environment Configuration · holobiomicslab

    Use when you need to execute a complex computational chemistry workflow (QCxMS2) that depends on multiple external semiempirical and ab initio quantum chemistry packages.
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15. ▌
    Transformation Method Comparison · holobiomicslab

    Use when when you have paired microbiome (16S rRNA or functional) and metabolome (LC-MS/MS or similar) data and must decide between compositional transformations (CLR, RA, or others) before training a predictive model.
    0 installs
16. ▌
    Unsupervised Spectrum Clustering · holobiomicslab

    Use when when you have high-dimensional embedding vectors from pretrained models (e.g., MSBERT) and need to verify that the learned representation space groups spectra by chemical similarity without labeled training data.
    0 installs
17. ▌
    Usi Spectrum Identifier Encoding · holobiomicslab

    Use when you have a Universal Spectrum Identifier (USI) string referencing a spectrum in a supported metabolomics repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, MassIVE, or MS2LDA) and need to create an embeddable, scannable reference for publication or data integration that.
    0 installs
18. ▌
    Web Application Endpoint Mapping · holobiomicslab

    Use when you have a user-submitted spectrum with associated domain context metadata (e.g., selected as 'microbial origin', 'plant tissue', 'food sample') and need to route that spectrum to the appropriate domain-specific MASST application for searching.
    0 installs
19. ▌
    Xcms Grouped Object Manipulation · holobiomicslab

    Use when you have preprocessed LC-MS data with detected chromatographic peaks that need to be consolidated into feature groups representing putative compounds.
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20. ▌
    Xcms Output Replacement Workflow · holobiomicslab

    Use when xCMS has produced aligned LC-MS features but alignment quality is suspected to be poor—especially when analyzing hundreds of samples, data acquired over extended periods (>1 week), or when individual m/z bins show inconsistent RT shifts.
    0 installs
21. ▌
    Bioassay Activity Data Integration · holobiomicslab

    Use when when you have (1) a molecular network graph from GNPS with node identifiers and edges, (2) LC-MS/MS features quantified across fractions in a feature table, and (3) bioassay measurements (e.
    0 installs
22. ▌
    In Silico Fragment M Z Calculation · holobiomicslab

    Use when when you have experimental UHPLC-HRMS/MS or direct infusion MS/MS data and need to identify lipid species by comparing observed fragment m/z values against a library of simulated fragments. Apply this skill when your lipid library is incomplete or specialized (e.
    0 installs
23. ▌
    In Silico Fragmentation Prediction · holobiomicslab

    Use when you have candidate metabolite structures (from database lookup or enumeration) and experimental MS/MS spectra (mzML, mzXML format), and need to rank candidates by how well their predicted fragments match observed peaks.
    0 installs
24. ▌
    Inadequate Spectral Interpretation · holobiomicslab

    Use when you have clustered peak networks from INADEQUATE NMR spectra (output from the Clustering module) and need to assign metabolite identities by comparing them to known spectral signatures.
    0 installs
25. ▌
    Top K Retrieval Ranking Evaluation · holobiomicslab

    Use when when you have deployed a trained embedding or similarity model on a test set of tandem mass spectra and need to measure its ability to rank correct library compounds near the top of retrieved candidates.
    0 installs
26. ▌
    Transfer Learning Encoder Freezing · holobiomicslab

    Use when you have a pretrained spectrum encoder (e.g., TCN on mass spectrometry data) that has learned useful representations, and you need to train new components (e.g., a rescoring module) for a related but distinct task (e.
    0 installs
27. ▌
    Treemap Visualization Construction · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, use this skill when you need to communicate the count and percentage breakdown of ions retained vs. rejected across filter status categories.
    0 installs
28. ▌
    Untargeted Metabolomics Annotation · holobiomicslab

    Use when you have authentic metabolite standards analyzed by LC-MS in both positive and negative ESI modes (converted to .
    0 installs
29. ▌
    Usi Spectrum Retrieval And Loading · holobiomicslab

    Use when you have a USI accession (e.g., 'mzspec:MSV000082283:f07074:scan:5475' or 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555') pointing to a publicly deposited tandem mass spectrometry scan in a GNPS or ProteomeXchange repository, and you need to retrieve and instantiate.
    0 installs
30. ▌
    Vendor Raw File Format Recognition · holobiomicslab

    Use when you have a directory containing mass spectrometry data files from multiple instrument vendors (Thermo, AB Sciex, Agilent, Bruker, etc.) and need to convert them to a common format (Aird or mzML).
    0 installs
31. ▌
    2d Nmr Pulse Sequence Implementation · holobiomicslab

    Use when when you need to generate 2D metabolomic NMR spectra (COSY for homonuclear or HSQC/HMQC for heteronuclear correlations) from parsed metabolite concentration and spin-system J-coupling data, and you want to simulate realistic peak patterns including indirect-dimension evolution and phase.
    0 installs
32. ▌
    Chemical Shift Coordinate Extraction · holobiomicslab

    Use when you have loaded an INADEQUATE NMR spectrum file and need to detect individual peaks (local maxima) across the chemical shift dimension with associated intensity values. This is the mandatory first processing step before filtering peaks into networks or matching against metabolite databases.
    0 installs
33. ▌
    Coefficient Of Variation Computation · holobiomicslab

    Use when you have loaded raw NMR or MS metabolomic abundance data into a SummarizedExperiment object and need to assess feature reproducibility before downstream association modeling.
    0 installs
34. ▌
    Container Image Build And Deployment · holobiomicslab

    Use when you have a Dockerfile and source repository for a bioinformatics tool (e.g., CloMet) and need to verify that the tool can be containerized, deployed, and made executable in an isolated environment.
    0 installs
35. ▌
    Cross Assay Feature Linkage Analysis · holobiomicslab

    Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple parallel assays acquired in complementary ionization modes (e.
    0 installs
36. ▌
    Graph Based Molecular Representation · holobiomicslab

    Use when when you have 1D NMR spectra (¹H and/or ¹³C) as input and need to predict complete molecular structure (both molecular formula and bond connectivity) for molecules with up to 19 heavy atoms.
    0 installs
37. ▌
    Lineshape Convolution And Broadening · holobiomicslab

    Use when after generating theoretical spin multiplets for individual metabolites via first-order or density-matrix NMR simulation, but before combining spectra or applying Fourier transformation.
    0 installs
38. ▌
    Mass Difference Network Construction · holobiomicslab

    Use when you have a preprocessed peak list (m/z values and assigned molecular formulas) from direct injection FT-ICR MS of a complex organic mixture (e.
    0 installs
39. ▌
    Modality Contribution Quantification · holobiomicslab

    Use when when you have a trained multitask model that accepts multiple input modalities (e.g., 1D NMR spectra in different nuclei or complementary analytical techniques) and you need to understand their relative importance for the downstream prediction task (e.g., molecular structure elucidation).
    0 installs
40. ▌
    Nmr Chemical Shift Interval Matching · holobiomicslab

    Use when you have isolated one or more regions-of-interest (ROIs) from a proton NMR spectrum (defined as lower and upper chemical-shift bounds in ppm) and need to systematically generate a list of plausible metabolite assignments from a reference database.
    0 installs
41. ▌
    Nmr Metabolite Identity Confirmation · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data with an unknown or ambiguous peak (e.g., at a specific chemical shift δ), and you need to determine its chemical identity.
    0 installs
42. ▌
    Nmr Spectrum Data Import And Parsing · holobiomicslab

    Use when you have raw 1D ¹H NMR spectroscopy output consisting of (1) a CSV file with chemical shift and intensity columns and (2) a TXT file listing detected peak chemical shifts, and you need to load and validate these into memory before passing them to a metabolite identification model like.
    0 installs
43. ▌
    Unannotated Feature Characterization · holobiomicslab

    Use when you have aligned feature tables from LC–MS/MS, corresponding in silico annotations (from GNPS/ISDB or SIRIUS), and metadata describing sample origin. Use it to rank extracts by the proportion of sample-specific, unannotated features—a proxy for structural novelty.
    0 installs
44. ▌
    Xcms Feature Extraction And Grouping · holobiomicslab

    Use when you have raw mzXML LC/MS files from replicated metabolomics experiments (e.g., 12 samples across labeled/unlabeled conditions) and need to extract, align, and group peaks before downstream feature filtering (e.g., fold-change or isotope enrichment analysis).
    0 installs
45. ▌
    Bedgraph File Format Manipulation · holobiomicslab

    Use when you have aligned ChIP-Seq reads (in BED or BEDPE format) and need to convert them into quantitative genome-wide signal tracks (coverage, p-value, or q-value scores) for downstream statistical comparison or peak detection.
    0 installs
46. ▌
    Bisulfite Sequencing Data Loading · holobiomicslab

    Use when you have raw methylation call files from Bismark, MethylDackel, or similar bisulfite alignment tools (bedGraph, cytosine report, or tabix-indexed formats) and need to import them into R as methylRaw or methylRawListDB objects for downstream differential methylation analysis, quality.
    0 installs
47. ▌
    Chip Seq Read Alignment Filtering · holobiomicslab

    Use when when beginning peak calling on ChIP-Seq data: you have raw single-end or paired-end BED/BEDPE alignment files for both ChIP and control samples and need to remove duplicate reads before predicting fragment length and building local bias models.
    0 installs
48. ▌
    Cpg Island Feature Classification · holobiomicslab

    Use when you have a methylDiff object containing differentially methylated bases or regions from bisulfite sequencing, gene annotation in BED or similar format (RefSeq, Ensembl), and CpG island coordinate files, and need to understand what fraction of your differential methylation signal falls.
    0 installs
49. ▌
    Dna Methylation Array Data Import · holobiomicslab

    Use when you have raw .idat files or beta-valued matrices from Illumina HumanMethylation450 (450K) or EPIC array experiments and need to import them into R for quality control and downstream analysis.
    0 installs
50. ▌
    Hi C Insulation Score Calculation · holobiomicslab

    Use when you have a cooler-format Hi-C contact matrix and need to identify TAD boundaries and insulation strength along the genome. Use this skill when your research question requires quantifying local chromatin compartmentalization or annotating structural domain edges for downstream analysis (e.
    0 installs
51. ▌
    Methylation Region Identification · holobiomicslab

    Use when you have loaded normalized methylation beta-value matrices from Illumina EPIC or 450k arrays and need to move beyond single-CpG differential methylation testing to identify multi-CpG regions with coordinated differential methylation signals.
    0 installs
52. ▌
    Motif Database Query And Matching · holobiomicslab

    Use when you have a set of differentially accessible peaks (output from differential accessibility testing, e.g., tl.
    0 installs
53. ▌
    Narrow Peak Coordinate Validation · holobiomicslab

    Use when after running macs3 callpeak with the -f BEDPE flag on paired-end ChIP-Seq data (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.
    0 installs
54. ▌
    Stream Trajectory Data Formatting · holobiomicslab

    Use when you have completed peak calling and cell annotation in ArchR and want to perform trajectory inference or visualization in STREAM. Apply it specifically when your analysis goal requires STREAM's specialized trajectory reconstruction methods (e.
    0 installs
55. ▌
    Z Score Based Statistical Testing · holobiomicslab

    Use when you have a sparse chromatin accessibility matrix (ATAC-seq or DNAse-seq counts per peak per sample), matched peak-annotation assignments (e.
    0 installs
56. ▌
    API Response Latency Measurement · holobiomicslab

    Use when when annotating .msp files with metadata from multiple external web services and you need to monitor which services are slow or unreliable.
    0 installs
57. ▌
    Backend Performance Benchmarking · holobiomicslab

    Use when when you have execution time data for visualization scripts across multiple backends (matplotlib, Bokeh, Plotly) and need to determine which backend offers the fastest median performance for specific mass spectrometry plot types (chromatogram, mobilogram, peakmap, peakmap-marginals.
    0 installs
58. ▌
    Bit Vector Substructure Encoding · holobiomicslab

    Use when you need to represent natural product molecules as fixed-length bit vectors for downstream machine learning (e.
    0 installs
59. ▌
    Calibration Residual Calculation · holobiomicslab

    Use when after a mass spectrum has been matched against a reference m/z file (e.g., SRFA.ref) and a sufficient number of calibration points (≥5) have been identified within a given PPM tolerance window.
    0 installs
60. ▌
    Chemical Structure Deduplication · holobiomicslab

    Use when after applying biotransformation rules to generate candidate product structures from input molecules, when the same transformed structure can be produced via multiple transformation pathways or rule applications, and you need a single canonical representation while tracking which rules and.
    0 installs
61. ▌
    Chemical Structure Featurization · holobiomicslab

    Use when you have SMILES strings or molecular structure files (e.g., from a synthetic drug database) and need to feed them into a deep learning model like PS2MS, NEIMS, or DeepEI that expects numerical feature vectors.
    0 installs
62. ▌
    Cheminformatics Library Querying · holobiomicslab

    Use when you have a list of query chemicals (compound names or SMILES) and a reference library organized by chemical groups (e.g., Types A–E, GroupA/GroupB), and you need to assess which library compounds are structurally similar to your queries, retrieve their categorical annotations (e.
    0 installs
63. ▌
    Data Format Conformance Checking · holobiomicslab

    Use when you have retrieved a complete set of project JSON documents from a data platform and need to verify that each document's structure, field types, and required properties match a canonical JSON Schema definition (e.g., app/public/schema.json).
    0 installs
64. ▌
    Database Accessor Initialization · holobiomicslab

    Use when a Python module declares optional/conditional dependencies (e.g., sqlalchemy for database access) and you need to confirm that the module can be imported and instantiated without exceptions when those dependencies are present in the environment.
    0 installs
65. ▌
    Descriptor Subgroup Partitioning · holobiomicslab

    Use when when you have a trained BitterPredict classifier, a dataset of molecules with computed descriptors and known bitter/not-bitter labels, and want to understand which descriptor categories (e.g., molecular weight, lipophilicity, topological, pharmacophoric) drive prediction decisions.
    0 installs
66. ▌
    Docker Image Registry Inspection · holobiomicslab

    Use when after building multiple Docker image variants (e.g., cli, dev, linux, windows) using multi-stage builds with --target flags, and you need to verify that each variant's size falls within documented ranges (e.g., cli 6–7 GB, dev 9–11 GB, linux 8–10 GB, windows 4–5 GB).
    0 installs
67. ▌
    Field Mapping And Transformation · holobiomicslab

    Use when converting intermediate JSONized experimental metadata (extracted from tagged tabular data) to a target repository format (e.
    0 installs
68. ▌
    Ion Image Embedding Optimization · holobiomicslab

    Use when you have 512-dimensional representation vectors output from ResNet18 encoders processing paired augmented ion images, and you need to prevent trivial solutions (representation collapse) during contrastive learning—specifically when optimizing for maximized similarity between augmentations.
    0 installs
69. ▌
    Lipid Species Abundance Counting · holobiomicslab

    Use when you have access to a lipidomics library repository (e.g., LipidMatch .csv files) and need to audit or report the total number of distinct lipid species and lipid-type categories present.
    0 installs
70. ▌
    Mass Action Kinetics Formulation · holobiomicslab

    Use when you have intracellular metabolomics concentration measurements across multiple cell lines or conditions, a stoichiometric metabolic network model with reaction-metabolite associations, and you need to predict how differences in substrate availability (independent of enzyme expression).
    0 installs
71. ▌
    Missing Data Simulation In Omics · holobiomicslab

    Use when when comparing the robustness of multiple pathway ranking methods (e.g., PLAGE, ORA, GSEA) on metabolomics or other omics data, and you need to establish which method is least sensitive to peak dropout, instrumental noise, or annotation uncertainty.
    0 installs
72. ▌
    Missing Value Imputation With Na · holobiomicslab

    Use when you are implementing a custom MsBackend subclass for the Spectra package and need to ensure that spectraData() returns all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of which ones are explicitly stored in your backend.
    0 installs
73. ▌
    Molecular Descriptor Calculation · holobiomicslab

    Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
    0 installs
74. ▌
    Msi Data Format Interoperability · holobiomicslab

    Use when your MSI data is stored in a Cardinal imaging experiment object (version 2.2+) that has already been peak-binned with peakBin(), and you want to run mass2adduct's massdiff() and adductMatch() pipeline without manually exporting to CSV;
    0 installs
75. ▌
    Neural Network Weight Extraction · holobiomicslab

    Use when you have trained MLPNN models on paired microbiome-metabolome data (via 10-fold cross-validation repeated across multiple iterations) and need to derive interpretable microbe-metabolite interaction scores rather than treating the network as a black box.
    0 installs
76. ▌
    Orchestrator Architecture Design · holobiomicslab

    Use when when building a multi-backend visualization library where users specify both a plot type (spectrum, chromatogram, peakmap) and a backend (matplotlib for static output, Bokeh or Plotly for interactive), and you need to avoid code duplication across backends while keeping the user-facing API.
    0 installs
77. ▌
    Peak Quality Threshold Filtering · holobiomicslab

    Use when after composite-map peak detection (scipy.signal.find_peaks) has identified candidate peaks on aligned mass tracks, but before compiling the final feature table.
    0 installs
78. ▌
    Python Environment Configuration · holobiomicslab

    Use when when you have installed a Python package (e.g., via pip or conda) and need to confirm that the installation succeeded and all expected submodules can be imported.
    0 installs
79. ▌
    Qc Sample Variability Assessment · holobiomicslab

    Use when after batch correction of a metabolomics dataset using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to systematically evaluate which one produces the most stable compound quantification (lowest QC variability) for each compound.
    0 installs
80. ▌
    Qc Workflow Component Inspection · holobiomicslab

    Use when you have acquired a versioned QC workflow definition file (YAML or JSON) from a metabolomics QC system release (e.g., v1.0.
    0 installs
81. ▌
    R Parallel Backend Configuration · holobiomicslab

    Use when you have multiple MSP (mass spectrum) library files to read and merge in R, and your computational task is time-consuming (e.g., structure extraction, SMILES assignment, or RI assignment) and you have a multi-core system available.
    0 installs
82. ▌
    Raw Data Throughput Benchmarking · holobiomicslab

    Use when when you have a raw mass spectrometry file (e.g., Thermo Orbitrap .raw) and need to establish the measured throughput of a spectral reading function (e.
    0 installs
83. ▌
    S4 Class Object Memory Profiling · holobiomicslab

    Use when when designing or optimizing S4-based data backends (such as MsBackend subclasses) and you need to decide whether to pre-populate all slots with complete data structures or defer initialization until data access.
    0 installs
84. ▌
    Software Testing Unit Validation · holobiomicslab

    Use when after making code modifications (bug fixes, new features, or refactoring) to the MS2Query codebase, or when contributing changes via pull request. The skill is essential before pushing feature branches to the repository or merging changes into master.
    0 installs
85. ▌
    Spectra Variable Core Population · holobiomicslab

    Use when when implementing a custom MsBackend and the spectraData() method needs to return all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of which variables were explicitly stored during backend initialization.
    0 installs
86. ▌
    Spectral Data Quality Assessment · holobiomicslab

    Use when importing raw or public mass spectrometry spectral data in formats such as MGF, MSP, or mzML that may contain incomplete metadata (e.g., missing instrument type, precursor m/z, retention time), low-intensity noise peaks, or spectra with invalid or inconsistent metadata fields.
    0 installs
87. ▌
    Structured Data Element Checking · holobiomicslab

    Use when you have generated or received a mass spectrometry data file in a structured format (e.g., mzPeak, Parquet-based archive) and need to verify it conforms to the published specification before use in analysis pipelines, sharing with collaborators, or publishing.
    0 installs
88. ▌
    Structured Inventory Compilation · holobiomicslab

    Use when when you need to understand the modular composition of a multi-component research software project, particularly before onboarding, refactoring, or deploying it.
    0 installs
89. ▌
    Syntax Tree Construction Parsing · holobiomicslab

    Use when you have a domain-specific language (DSL) grammar specification and raw query strings that must be converted into structured intermediate representations for validation, transformation, or execution.
    0 installs
90. ▌
    Aggregate Statistics Computation · holobiomicslab

    Use when you have a validated or curated dataset (e.g., a TSV or gzip-compressed tabular file) and need to produce summary counts: unique curated structures (separately for 3D and 2D representations), unique organisms, and unique structure-organism pair combinations.
    0 installs
91. ▌
    Ancova Peak Association Analysis · holobiomicslab

    Use when when you have preprocessed metabolomics peak tables (feature matrix with samples × peaks) and sample metadata (phenotype/grouping information and optional continuous covariates), and your research question is to identify which peaks differ significantly between groups while accounting for.
    0 installs
92. ▌
    Bgc Feature Vector Normalization · holobiomicslab

    Use when when you have pre-computed BGC feature vectors (from domain architecture extraction) and need to cluster them into GCFs using BiG-SLiCE v2.
    0 installs
93. ▌
    Binary Representation Generation · holobiomicslab

    Use when you have raw mass spectra data (MGF format with m/z/intensity pairs) that need to be clustered rapidly, especially on large-scale proteomics datasets (millions of spectra).
    0 installs
94. ▌
    Biomarker Coefficient Extraction · holobiomicslab

    Use when after normalizing a log-transformed metabolomics featuredata matrix (with missing values imputed via knn or replacement) and encoding experimental factors into a design matrix (factormat), use this skill to fit a linear model and extract per-metabolite coefficients and p-values for each.
    0 installs
95. ▌
    Bruker Mass Spectrum Data Import · holobiomicslab

    Use when you have received a Bruker Solarix FT-ICR raw data directory (.d format, containing CompassXtract output or native ser/fid transients) and need to import it into a Python-based analysis workflow for FT-MS signal processing, calibration, or molecular formula search.
    0 installs
96. ▌
    Building Block Annotation Export · holobiomicslab

    Use when you have retrieved a user database entry (sequence or building-block structure record) from the MassSpecBlocks backend and need to generate a file in CycloBranch format for mass spectra analysis, interpretation, or sharing with collaborators using the CycloBranch software.
    0 installs
97. ▌
    Chemical Class Novelty Detection · holobiomicslab

    Use when when you have CANOPUS chemical class predictions for your samples and need to identify which extracts contain chemical classes absent from the literature for their species or genus.
    0 installs
98. ▌
    Chemical Structure Serialization · holobiomicslab

    Use when you need to export a stored chemical structure (sequence or building-block entry) from the MassSpecBlocks database to enable mass spectra analysis in CycloBranch or when preparing structures for import into other cheminformatics workflows that require a standardized structure interchange.
    0 installs
99. ▌
    Cheminformatics Table Generation · holobiomicslab

    Use when when you have standardized molecular structures (SMILES or SDF format) and need to compute molecular fingerprint bits and chemical property descriptors for downstream retention time prediction, molecular classification, or machine-learning-based identification tasks.
    0 installs
100. ▌
     Chromatographic Data Structuring · holobiomicslab

     Use when after parsing a centroid mzML file into (m/z, scan_number, intensity) tuples, when you need to organize sparse MS1 data for efficient peak detection and cross-sample alignment. Apply this skill when high mass resolution (e.
     0 installs