← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 11k skills
• 0 followers
• last month last updated

1. ▌
   Spectra Data Representation Backends 2 · holobiomicslab

   Use when you are creating a new backend to expose MS data (m/z, intensity, retention time, and other spectral properties) from a specific storage format or data source (e.g., mzML files, SQL databases, in-memory matrices, or spectral libraries) to Spectra objects.
   0 installs
2. ▌
   Spectral Feature Chemical Assignment 2 · holobiomicslab

   Use when you have spectral feature data annotated by both in silico structural tools (e.
   0 installs
3. ▌
   Spectral Metadata Enrichment Via API 2 · holobiomicslab

   Use when you have .msp spectrum files with minimal metadata (e.g., only compound name and mass) and need to augment them with chemical structure descriptors, identifiers, and properties from external databases.
   0 installs
4. ▌
   Structure Ranking From Spectral Data 2 · holobiomicslab

   Use when you have an experimental tandem mass spectrum (collision-induced dissociation or ESI-MS/MS) and a chemical formula, and you need to identify the correct structure among multiple isomeric candidates in a database like PubChem.
   0 installs
5. ▌
   Tree Structural Integrity Assessment 2 · holobiomicslab

   Use when after generating a Chemical Feature Tree artifact (Phylogeny[Rooted]) from q2-qemistree's make-hierarchy method, or when importing a tree from external sources, to confirm it is well-formed before proceeding to alpha/beta-diversity analysis.
   0 installs
6. ▌
   Unannotated Feature Characterization 3 · 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
7. ▌
   Unit Test Design For Data Processing 2 · holobiomicslab

   Use when building or extending a data extraction and conversion system (such as MESSES) where tabular data is transformed via conversion directives into JSON intermediate formats and then into domain-specific schemas.
   0 installs
8. ▌
   Xcms Feature Extraction And Grouping 3 · 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
9. ▌
   XML Structured Metadata Construction 2 · holobiomicslab

   Use when when you have synthesized or assembled mass spectrometry spectral data (m/z values, intensities, retention times) and need to encode it as a portable, standard mzML file format rather than a proprietary binary or text representation.
   0 installs
10. ▌
    Aromaticity Index Computation 2 · holobiomicslab

    Use when after molecular formula assignment from FT-ICR MS peaks and elemental composition tabulation (C, H, O, N, S, P counts), when you need to quantify the degree of aromaticity and carbon-skeleton unsaturation for each detected compound to support Van Krevelen classification, chemodiversity.
    0 installs
11. ▌
    Interactive Plot Rendering Bokeh 2 · holobiomicslab

    Use when when you have mass spectrometry data in a Pandas DataFrame with columns for m/z, retention time (or ion mobility), and intensity, and you want to generate interactive (rather than static) visualizations for exploratory analysis, interactive drill-down, or deployment in web applications or.
    0 installs
12. ▌
    Concentration Based Signal Scaling 2 · holobiomicslab

    Use when you have loaded m/z peak data with metadata that includes a concentration column representing sample loading mass or volume, and systematic intensity variation across samples is suspected to reflect preparation differences rather than true biological variation.
    0 installs
13. ▌
    Data Quality Validation Lipidomics 2 · holobiomicslab

    Use when after loading and parsing raw MRM export files (TSV, CSV, or vendor-specific formats) into a pandas DataFrame and decomposing lipid nomenclature, before performing lipid matching, statistical analysis, or visualization.
    0 installs
14. ▌
    Dot Product Similarity Computation 2 · holobiomicslab

    Use when when performing open modification spectral library searching and you need to sensitively match query spectra that may carry unknown post-translational or chemical modifications to an unmodified spectral library.
    0 installs
15. ▌
    External Calibration Model Fitting 2 · holobiomicslab

    Use when you have acquired targeted mass spectrometry data with measured ion intensities for known standard compounds at multiple concentration levels, and you need to convert sample intensities into absolute or relative concentrations.
    0 installs
16. ▌
    Interactive Plot Axis Selection UI 2 · holobiomicslab

    Use when when you have a high-resolution mass spectrometry dataset with m/z values and need to generate Kendrick mass plots where users should choose between plotting raw m/z or computed Normalized Kendrick Mass (NKM) on the x-axis.
    0 installs
17. ▌
    Msms Spectrum Object Instantiation 2 · holobiomicslab

    Use when when you have successfully resolved a USI string to extract raw spectrum data from an online proteomics/metabolomics repository (PRIDE, MassIVE, etc.) and need to construct a spectrum object that exposes spectrum data as Python attributes and methods for downstream processing (filtering.
    0 installs
18. ▌
    Peak Detection Accuracy Assessment 2 · holobiomicslab

    Use when after running a non-targeted preprocessing (NPP) pipeline (e.g., XCMS, MZmine 2, OpenMS) on the same set of centroided mzML files that were used to generate a validated benchmark dataset.
    0 installs
19. ▌
    Psm To Spectrum Linking Validation 2 · holobiomicslab

    Use when when you have PSM files from a proteomics search engine (e.g., MaxQuant, MSGFPlus, Mascot) and corresponding spectrum files (mzML or MGF format) that need to be linked before rescoring.
    0 installs
20. ▌
    Python Binary Io And Serialization 2 · holobiomicslab

    Use when when you have mzPeak files (Parquet-based archives in uncompressed ZIP containers) or other PyArrow-compatible columnar formats containing mass spectrometry spectra, and you need to extract and decode spectral data arrays (m/z values, intensities) into Python memory for downstream.
    0 installs
21. ▌
    Spectra Variable Metadata Handling 2 · holobiomicslab

    Use when when designing a new MsBackend subclass or extending an existing backend to support mass spectrometry data import or representation.
    0 installs
22. ▌
    Unsaturation Degree Quantification 2 · holobiomicslab

    Use when you have FT-ICR MS peak data with assigned molecular formulas (C, H, O, N, S, P elemental counts) and want to characterize the structural saturation and aromaticity of metabolites to assess their biochemical degradation potential, compare chemodiversity across samples, or stratify.
    0 installs
23. ▌
    User Override Parameter Management 2 · holobiomicslab

    Use when punc'data's automatic keyword-based column recognition produces incorrect semantic role assignments—for example, when a column header contains a non-standard keyword that the tool fails to recognize, or when a column's true semantic role (e.
    0 installs
24. ▌
    Histogram Peak Occurrence Analysis 2 · holobiomicslab

    Use when after you have computed a histogram of pairwise mass differences from MSI peak data and want to identify which mass shifts occur most frequently and whether they correspond to known chemical adducts.
    0 installs
25. ▌
    Spatio Molecular Matrix Processing 2 · holobiomicslab

    Use when you have deposited SpaceM spatio-molecular matrices (MORPHnMOL.
    0 installs
26. ▌
    Spectral Search Result Aggregation 2 · holobiomicslab

    Use when when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to consolidate results across domains (e.
    0 installs
27. ▌
    Adduct Assignment Accuracy Assessment 2 · holobiomicslab

    Use when you have a trained formula ranking model (such as MIST-CF) and want to measure the specific performance gain from incorporating multiple positive-mode adduct types (e.g., [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+) instead of restricting predictions to [M+H]+ only.
    0 installs
28. ▌
    Aird Format Conversion And Validation 2 · holobiomicslab

    Use when you have vendor mass spectrometry raw files (e.g., .raw, .d, .
    0 installs
29. ▌
    Cosine Similarity Spectral Clustering 3 · holobiomicslab

    Use when you have a collection of deconvolved mass spectra (in MGF or mzTab format) from GC-MS analysis and need to group them into a molecular network to identify structural relationships and enable compound annotation.
    0 installs
30. ▌
    Extracted Ion Chromatogram Processing 2 · holobiomicslab

    Use when you have Thermo Fisher Orbitrap .raw files and need to locate and quantify specific peptide precursor ions (e.g., iRT calibrants, synthetic standards, or putative identifications).
    0 installs
31. ▌
    Mass Charge Retention Time Validation 2 · holobiomicslab

    Use when after loading centroided .mzML LC-MS data and creating a target list with compound ID, name, theoretical or measured m/z, expected RT (in minutes), and polarity designation, perform this validation step to confirm target visibility and refine m/z and RT window parameters before running.
    0 installs
32. ▌
    Mass Spectrometry Compound Extraction 2 · holobiomicslab

    Use when you have a preprocessed GC-MS dataset (from spreadOut) with standardized column names (Compound.Name, Component.RT, Base.Peak.MZ, Component.Area, Match.Factor) and a specific list of chemical compounds you want to extract and aggregate across multiple sample runs.
    0 installs
33. ▌
    Mass Spectrometry Data Representation 2 · holobiomicslab

    Use when you need to store or retrieve mass spectrometry spectra (m/z and intensity pairs) from a novel data source or storage medium (e.
    0 installs
34. ▌
    Mass Spectrometry File Format Parsing 3 · holobiomicslab

    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.
    0 installs
35. ▌
    Mass Spectrometry Peak Classification 2 · holobiomicslab

    Use when you have raw mzML files and feature tables (CSV format from mzMine or XCMS) from untargeted LCMS experiments and need to distinguish true metabolite peaks from false positives introduced by the peak-picking algorithm.
    0 installs
36. ▌
    Metabologenomic Database Construction 2 · holobiomicslab

    Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified peptides (RiPPs) by integrating genomic and mass spectrometry data.
    0 installs
37. ▌
    Metabolomic Feature Tree Construction 2 · holobiomicslab

    Use when when you have preprocessed LC-MS/MS data (MGF file with MS1 and MS2 spectra and a feature abundance table from MZmine2 or similar peak detection tool) and need to perform chemical phylogeny-based diversity analyses or meta-analyses comparing metabolomic profiles across multiple samples or.
    0 installs
38. ▌
    Metadata Harmonization Across Sources 2 · holobiomicslab

    Use when you have completed independent batch searches across one or more domain-specific MASST tools (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and received multiple separate output files (_microbe.html, _plant.json, _matches.tsv, _library.tsv, _datasets.tsv, _count_domain.
    0 installs
39. ▌
    Module Dispatch Architecture Analysis 3 · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (like mzmine) decides which processing module receives a given dataset based on its declared data type (LC vs. GC vs. IMS vs. MS imaging).
    0 installs
40. ▌
    Precursor Peak Removal Mass Tolerance 2 · holobiomicslab

    Use when after loading an MsmsSpectrum object but before intensity filtering or spectral annotation.
    0 installs
41. ▌
    Reaction Propensity Score Computation 2 · holobiomicslab

    Use when you have measured intracellular metabolite abundances (LC-MS or similar) across multiple cell lines or conditions and a stoichiometric metabolic model (with reaction-metabolite associations) to estimate how differences in substrate availability—independent of gene expression—translate into.
    0 installs
42. ▌
    Retention Time And Mz Based Alignment 2 · holobiomicslab

    Use when after peak detection has been completed on individual LC-MS samples and you have a collection of detected peaks with m/z, retention time, and intensity values from each sample.
    0 installs
43. ▌
    Routing Module Testing And Validation 2 · holobiomicslab

    Use when when you have implemented conditional routing logic in the GNPS_MASST codebase and need to verify that spectrum submissions with explicit domain-context selections (e.
    0 installs
44. ▌
    Subformula Assignment Neural Networks 2 · holobiomicslab

    Use when when you have MS/MS spectra with assigned precursor formulas and need to annotate fragment peaks with their chemical subformulas, but want to avoid the computational overhead of generating full SIRIUS fragmentation trees or do not have access to spectrum databases.
    0 installs
45. ▌
    Tanimoto Score Threshold Optimization 2 · holobiomicslab

    Use when when you have a set of MS/MS spectra with ground-truth structural similarity labels (Tanimoto scores computed from molecular fingerprints) and need to choose a decision threshold for classifying spectrum pairs as 'chemically related' or 'unrelated'.
    0 installs
46. ▌
    Backend Performance Tradeoff Analysis 2 · holobiomicslab

    Use when you are designing or optimizing an MsBackend implementation and need to decide whether to pre-populate the @spectraVars slot with all core spectra variable columns (mz, intensity, rtime, scanIndex, precursorMz, precursorIntensity, acquisitionNum, msLevel) at initialization time, or defer.
    0 installs
47. ▌
    Browser Security Policy Configuration 2 · holobiomicslab

    Use when you need to run a web application locally (by opening index.html directly in the browser) and the application uses WebWorker or WebAssembly modules that fail to load with cross-origin policy or file-access errors.
    2 installs
48. ▌
    Combination Function Parameterisation 2 · holobiomicslab

    Use when you have two or more independent, standardised scoring functions that rank the same set of candidate pairs (e.
    0 installs
49. ▌
    Compound Database Lookup And Curation 2 · holobiomicslab

    Use when after feature extraction from LC–MS raw data (via XCMS, MS-Dial, or equivalent) has yielded a feature intensity table (samples × features) and feature metadata table (m/z, retention time, feature ID).
    0 installs
50. ▌
    Configuration Driven Batch Processing 2 · holobiomicslab

    Use when when processing multiple PSM files from search engines (e.g., MaxQuant, MSGFPlus, Mascot) that omit fixed modifications from their output, or when PSM and spectrum files use inconsistent ID schemes, decoy naming conventions, or modification notations.
    0 installs
51. ▌
    Corpus Size Coverage Scaling Analysis 4 · holobiomicslab

    Use when when deploying a Word2Vec-based spectral similarity model (such as Spec2Vec) on a new mass spectrometry dataset and needing to assess whether the pre-trained model's learned peak embeddings sufficiently represent the peaks in your query spectra.
    0 installs
52. ▌
    Cross Script Consistency Verification 2 · holobiomicslab

    Use when when a deep learning pipeline processes mass spectrometry spectra through multiple independent scripts (e.g., train_rescore.py, run_fiddle.py, test_caffeine.py) and a specific feature must be removed or masked to prevent the model from learning directly from a protected input (e.
    0 installs
53. ▌
    Cross Validation Benchmark Evaluation 2 · holobiomicslab

    Use when you have developed a predictive model and need to compare its performance against established baselines (e.g., linear regression, Random Forest, Canonical Correlation Analysis) across multiple datasets with paired input-output features.
    0 installs
54. ▌
    Dda Fragmentation Strategy Simulation 2 · holobiomicslab

    Use when you have real mzML LC-MS/MS data (e.g., from a Beer sample or HMDB reference set) and want to test whether a proposed TopN DDA strategy (or variant) can accurately reproduce the observed acquisition patterns, or you want to compare multiple acquisition controllers on the same chemical.
    0 installs
55. ▌
    Domain Context To Application Routing 2 · holobiomicslab

    Use when when a user submits one or more MS/MS spectra and has declared or implied a domain context (microbial, plant, tissue, microbiome, food, or metadata aggregation), and the search must be executed against the appropriate domain-curated spectral library.
    0 installs
56. ▌
    Heavy Isotope Labeling Interpretation 2 · holobiomicslab

    Use when your peptide sample has been enriched with stable isotope labels (13C, 15N, etc.) at a known incorporation probability (e.g., 52% 13C).
    0 installs
57. ▌
    Hotelling T Squared Outlier Detection 2 · holobiomicslab

    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.
    0 installs
58. ▌
    Ion Mobility Mobilogram Visualization 2 · holobiomicslab

    Use when when you have mass spectrometry data with ion mobility (drift time or 1/K₀) measurements as a continuous dimension and want to visualize intensity distributions across the ion mobility axis.
    0 installs
59. ▌
    Lc Ms Feature Alignment Cross Dataset 2 · holobiomicslab

    Use when you have two peak-picked, conventionally aligned LC-MS metabolomics datasets (e.
    0 installs
60. ▌
    Mass Spectrometry Data Format Parsing 3 · holobiomicslab

    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.
    0 installs
61. ▌
    Mass Spectrometry Screening Workflows 3 · holobiomicslab

    Use when when you have high-resolution LC-MS or GC-MS data from environmental samples and need to simultaneously screen for both known suspect chemicals and their transformation products, rather than targeting single compounds.
    0 installs
62. ▌
    Metabolite Abundance Drift Correction 2 · holobiomicslab

    Use when you have a raw LCMS nontargeted metabolomics abundance table spanning multiple injections with embedded pooled technical replicate (PREF) or internal standard injections distributed across the run sequence.
    0 installs
63. ▌
    Metabolite Pathway Annotation Mapping 2 · holobiomicslab

    Use when after peak detection and statistical association or classification analysis has identified a set of significant peaks, use this skill when you need to move from individual feature-level results (peak intensities, p-values, importance scores) to functional biological interpretation via.
    0 installs
64. ▌
    Metabolomics Feature Table Conversion 2 · holobiomicslab

    Use when you have generated a feature table via mzrtsim() with simulated LC/GC-MS abundances, condition assignments, and batch labels, and you need to pass it to Bioconductor tools (e.g., for batch correction, normalization, or statistical analysis) that expect SummarizedExperiment-class input.
    0 installs
65. ▌
    Multidimensional Coordinate Alignment 3 · holobiomicslab

    Use when you have detected feature tables from two or more LC-IMS-MS/MS samples (each containing m/z, drift_time, retention_time, and intensity measurements) and need to identify which features correspond to the same chemical compound across samples.
    0 installs
66. ▌
    Natural Isotope Abundance Propagation 2 · holobiomicslab

    Use when you have LC-MS fractional abundances of measured isotopologues (FAM) from a stable isotope labeling experiment and need to recover the true mass distribution vectors (MDV) that reflect only the contribution from the isotopic tracer. Use this skill when naturally occurring isotopes (e.
    0 installs
67. ▌
    Neural Network Architecture Extension 2 · holobiomicslab

    Use when you have a working base MPNN model (e.g., chemprop) and need to add task-specific feature processing layers (spectral, electronic, or domain features) to improve predictions on a specialized molecular property or spectrum.
    0 installs
68. ▌
    Ora Statistical Background Definition 2 · holobiomicslab

    Use when you are implementing ORA for metabolomics pathway analysis and must decide which metabolites constitute the statistical background against which to test your experimental detection list.
    0 installs
69. ▌
    Peak Picking Performance Benchmarking 2 · holobiomicslab

    Use when when you have completed non-targeted peak picking and alignment with tools such as MZmine 2, XCMS, or MS-DIAL on LC-HRMS mzML data and need to quantify performance metrics (found peaks %, degenerated isotopologue ratio, alignment errors) by comparing against a curated benchmark of known.
    0 installs
70. ▌
    Peak Property Dictionary Construction 2 · holobiomicslab

    Use when when you have identified the set of analytes (peptides, nucleosides, or other biomolecules) you wish to simulate in silico, and you need to prepare their chemical properties (m/z, intensity, retention time) in a machine-readable format before applying fragmentation and noise injection.
    0 installs
71. ▌
    Peptide Isotopic Envelope Calculation 2 · holobiomicslab

    Use when you have a peptide sequence, precursor charge state, and observed m/z spectrum and need to generate the expected isotopic distribution to match against observed precursor or fragment ion peaks. This is especially critical in SIP workflows where incorporation probabilities (e.g., 0.
    0 installs
72. ▌
    Rc Object Construction And Validation 2 · holobiomicslab

    Use when after feature detection and alignment (XCMS or equivalent), when you have a CSV feature table with m/z and retention time columns and need to group features derived from the same compound.
    0 installs
73. ▌
    Repository Cloning And Initialization 2 · holobiomicslab

    Use when you have a GitHub repository URL, a documented Python version requirement, and a list of pinned package versions, and you need to verify that the application will initialize without import or runtime errors before proceeding to data analysis or method replication.
    0 installs
74. ▌
    Spectral Library Integration Workflow 2 · holobiomicslab

    Use when when you have experimental UHPLC-HRMS/MS data targeting lipid species not adequately covered by LipidMatch's built-in library (500,000+ species across 60+ lipid types), or when working with specialized applications requiring custom lipid definitions (e.
    0 installs
75. ▌
    Spectral Library Match Classification 2 · holobiomicslab

    Use when when you have run MS2Query on query MS/MS spectra and obtained results with library matches that need to be disambiguated into two categories: (1) exact matches (precursor m/z difference near zero) versus (2) analog matches (chemically related but different precursor m/z).
    0 installs
76. ▌
    Spectral Library Matching And Ranking 2 · holobiomicslab

    Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a reference library.
    0 installs
77. ▌
    Spectral Similarity Score Computation 2 · holobiomicslab

    Use when when you have pairs of MS/MS spectra (in mgf, msp, mzml, mzxml, json, or usi format) and need to retrieve structurally related compounds or rank spectral similarity on a continuous scale (Tanimoto prediction).
    0 installs
78. ▌
    Statistical Visualization Multi Group 2 · holobiomicslab

    Use when when you have loaded search results from two or more DIA-MS analysis tools (e.
    0 installs
79. ▌
    Summary Statistics Table Construction 2 · holobiomicslab

    Use when when you need to quantify and compare the effect of multiple filtering thresholds (e.g., Match.Factor ≥65, ≥80, ≥90) on the size of a retained compound set.
    0 installs
80. ▌
    Tensor Operation Element Wise Product 2 · holobiomicslab

    Use when you have two embedding tensors of identical shape (e.g., both 512-dimensional) and need to produce a fused representation that captures multiplicative interactions between modalities.
    0 installs
81. ▌
    Transformation Product Parent Linkage 2 · holobiomicslab

    Use when after suspect screening has identified both parent features (from before-treatment or reference samples) and TP candidate features (from after-treatment or exposed samples) in the same analysis set, and you have MS/MS spectral data or formula annotations available.
    0 installs
82. ▌
    Large Scale Database Construction 2 · holobiomicslab

    Use when you have a collection of molecular structures (as SMILES or SDF files) and need to generate pre-computed CCS values for fast retrieval in downstream mass spectrometry workflows.
    0 installs
83. ▌
    Twim Instrument Offset Correction 2 · holobiomicslab

    Use when you have raw TWIM-MS data with arrival times (detector timestamps) rather than drift times, and you need to calibrate collision cross section values. TWIM platforms inherently record arrival time, not drift time, so this correction must precede CCS calibration workflows.
    0 installs
84. ▌
    Cascade Search Strategy Fdr Control 2 · holobiomicslab

    Use when when searching high-resolution mass spectra against spectral libraries and you need to identify both unmodified and post-translationally modified peptides while maintaining strict control over false positive identifications.
    0 installs
85. ▌
    Cross Reference Publication Linking 3 · holobiomicslab

    Use when when cataloging a suite of related bioinformatics tools or web applications (particularly in domains like metabolomics, microbiology, or systems biology) and you need to establish the authoritative peer-reviewed or preprint publication for each tool, verify publication URLs are live, and.
    0 installs
86. ▌
    Data Column Recognition And Mapping 2 · holobiomicslab

    Use when when uploading a delimited CSV or similar tabular file to Punc'data containing high-resolution mass spectrometry results, and the column headers are present but their semantic roles (e.
    0 installs
87. ▌
    Data Handoff Pipeline Orchestration 2 · holobiomicslab

    Use when you have raw MS files (with associated metadata: filename, upload path, file format) staged in an uploader repository and need to route them to a proteomics processor for analysis while preserving audit trails and ensuring format compatibility before processing begins.
    0 installs
88. ▌
    M Z Retention Time Feature Matching 2 · holobiomicslab

    Use when after extracting a feature table from XCMS, MS-Dial, or similar tools, when you possess a reference compound database with known m/z, retention time, and metadata, and you need to assign high-confidence (AnnoLevel 1) compound identities.
    0 installs
89. ▌
    Mass Spectrometry Format Conversion 2 · holobiomicslab

    Use when when you have mass spectrometry spectra in one of the six supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to convert them to a different format for compatibility with downstream tools, or when importing raw spectra into matchms for the first time and need to.
    0 installs
90. ▌
    Mass Spectrometry Peak Data Loading 2 · holobiomicslab

    Use when when you have raw or parsed MS spectra data (m/z values, intensity values, and spectral metadata) and need to integrate it into a Spectra object for downstream processing.
    0 installs
91. ▌
    Mass Spectrometry Raw File Handling 2 · holobiomicslab

    Use when you have raw MS data files from Thermo Orbitrap or other vendor instruments that must be uploaded into a centralized platform for automated processing. Use it at the start of a multi-stage omics workflow where data collection, management, processing, and visualization are integrated;
    0 installs
92. ▌
    Molecular Formula Search Assignment 2 · holobiomicslab

    Use when you have a recalibrated FT-ICR mass spectrum (Bruker .d format or equivalent) with detected, noise-thresholded peaks and need to assign chemical formulas to each peak. This is particularly relevant when analyzing samples with unknown composition (e.
    0 installs
93. ▌
    Python Random Access Implementation 2 · holobiomicslab

    Use when when you have an indexed gzip file (mzML.gz with internal index structure) and need to retrieve individual spectra or chromatograms by integer index without decompressing the entire file.
    0 installs
94. ▌
    Rdkit Molecular Property Extraction 2 · holobiomicslab

    Use when when you have a set of compounds represented as SMILES strings and need to compute their molecular properties (neutral mass, adduct-adjusted masses, mordred descriptors) for comparison against experimental peaks, retention time predictions, or similarity-based filtering thresholds during.
    0 installs
95. ▌
    Adduct Ion Parent Ion Pairing Analysis 3 · holobiomicslab

    Use when when you have binned mass spectrometry imaging peaks and want to understand which detected mass-to-charge ratios represent the same metabolite in different ionization states (parent vs. adduct form).
    0 installs
96. ▌
    Constraint Based Flux Balance Analysis 2 · holobiomicslab

    Use when you have a generic genome-scale metabolic model (SBML format) and cross-sectional omics data (RNA-seq, intracellular metabolomics, extracellular flux measurements from bioanalyzer or similar) from multiple biological samples (cell lines, conditions).
    0 installs
97. ▌
    Container Image Selection And Mounting 2 · holobiomicslab

    Use when when deploying a Nextflow workflow across multiple execution environments (local machines, HPC clusters) where tool versions, dependencies, or OS configurations may differ. Choose this skill specifically when you need to process LC-HRMS .mzML or .
    0 installs
98. ▌
    Cross Tool Result Concordance Analysis 2 · holobiomicslab

    Use when you have executed multiple NPDtools database search pipelines (Dereplicator, VarQuest, Dereplicator+, or MetaMiner in different modes) on identical test spectra or RiPP sequence inputs and need to understand their relative sensitivity, specificity, and complementarity.
    0 installs
99. ▌
    Lc Ms Feature Grouping And Compounding 3 · holobiomicslab

    Use when after chromatographic peak detection on preprocessed LC-MS data, when you have hundreds or thousands of individual m/z × retention-time peaks and need to associate them into biologically meaningful feature groups.
    0 installs
100. ▌
     Mass Spectrometry File Format Handling 2 · holobiomicslab

     Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g., from Q Exactive HF instruments) and need to extract spectral, chromatographic, or metadata directly into R for downstream statistical analysis, benchmarking, or integration with Bioconductor workflows.
     0 installs