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HolobiomicsLab

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1. ▌
   API Specification Extraction 2 · holobiomicslab

   Use when you have access to the source code of a webservice component (Python, configuration files, route definitions) and need to produce machine-readable API documentation (OpenAPI 3.
   0 installs
2. ▌
   Backend Routing And Dispatch 2 · holobiomicslab

   Use when you need to support multiple plotting backends for the same data visualization task, and you want to centralize backend selection logic so that users can specify their preferred rendering engine (matplotlib, bokeh, or plotly) at call time without modifying the core plotting logic.
   0 installs
3. ▌
   Baseline Comparison Analysis 3 · holobiomicslab

   Use when when you have trained a candidate model (e.g., an ensemble, a new architecture) and need to demonstrate its advantage over published or reference implementations on the same test data.
   0 installs
4. ▌
   Bond Connectivity Prediction 2 · holobiomicslab

   Use when you have predicted or partially assembled molecular fragments (as token sequences or substructure embeddings) and need to determine which atoms are bonded to which—that is, when the formula (atom inventory) is known or predicted but the connectivity graph is uncertain.
   0 installs
5. ▌
   Chemical Formula Enumeration 2 · holobiomicslab

   Use when you have an unknown MS/MS spectrum with a measured precursor m/z and want to generate a list of plausible chemical formula–adduct pairs to rank or filter downstream.
   0 installs
6. ▌
   Cloud Compatible File Output 2 · holobiomicslab

   Use when after feature clustering and drift correction (Gravity and Blueshift outputs) are complete and you need to produce a final, validated feature table ready for storage, archival, or downstream analysis.
   0 installs
7. ▌
   Column Name Variant Matching 2 · holobiomicslab

   Use when when processing mwTab metabolomics data files with variable column naming conventions (e.
   0 installs
8. ▌
   Conditional Dispatch Routing 2 · holobiomicslab

   Use when you have received a peak/feature table from an unknown or variable upstream peak-picking tool and need to ingest it into LipidMatch or a similar unified workflow. The input file format, column naming, or metadata structure is tool-specific (e.
   0 installs
9. ▌
   Configuration Object Pattern 2 · holobiomicslab

   Use when when designing a library that needs to support multiple plotting backends (e.g., matplotlib, bokeh, plotly) and you want to avoid reimplementing parameter validation, storage, and dispatch logic for each backend.
   0 installs
10. ▌
    Conversion Directive Parsing 2 · holobiomicslab

    Use when you have validated intermediate JSON data (conforming to the Experiment Description Specification) and need to configure how it should be converted to a supported output format (e.g., mwTab for Metabolomics Workbench submission).
    0 installs
11. ▌
    CSV To Dictionary Conversion 2 · holobiomicslab

    Use when you have a CSV file containing molecule definitions (chemical formula, m/z, intensity, retention time, or other peak properties) and need to prepare it for SMITER's simulation workflow.
    0 installs
12. ▌
    Electronic Noise Ion Removal 2 · holobiomicslab

    Use when working with raw MS/MS spectra that contain ions with repeated (identical) intensity values—a hallmark of electronic noise rather than true metabolite fragments.
    0 installs
13. ▌
    Energy Based Formula Scoring 2 · holobiomicslab

    Use when you have an unknown MS/MS spectrum (precursor m/z and fragment peak list) and a set of candidate molecular formulae, and you need to rank them by likelihood without access to a spectrum database or precomputed fragmentation trees.
    0 installs
14. ▌
    Energy Based Model Inference 2 · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (m/z and intensity pairs) and need to assign a chemical formula and ionization adduct to the precursor mass, particularly when spectrum database lookups are unavailable or when you want to exploit learned patterns in fragmentation rather than.
    0 installs
15. ▌
    Enrichment Ratio Calculation 2 · holobiomicslab

    Use when after generating combined or alternative scores for a set of BGC-metabolite (GCF-MF) link candidates, you need to evaluate whether a scoring function preferentially ranks true validated links higher than spurious ones.
    0 installs
16. ▌
    Export Tag Syntax Validation 2 · holobiomicslab

    Use when you have a tabular file (CSV or Excel) that has been manually or semi-automatically tagged with export tags, and you need to verify tag correctness before running the extract command to convert the tagged table into intermediate JSON.
    0 installs
17. ▌
    False Discovery Rate Control 2 · holobiomicslab

    Use when you have generated candidate peptide-spectrum matches from a spectral library search (especially open modification searches using cascade strategies) and need to assign statistical confidence to those matches. Use it whenever the scoring metric (e.
    0 installs
18. ▌
    Gc Ms Spectral Preprocessing 2 · holobiomicslab

    Use when you have raw GC-MS data files containing overlapped peaks (unresolved components with coeluting retention times) and need to predict pure mass spectra for each individual component using a Transformer-based model.
    0 installs
19. ▌
    Github Repository Operations 2 · holobiomicslab

    Use when when you need to verify that a software package (such as MassQL) passes its periodic integration test suite as indicated by CI workflow badges in the project documentation, or when you must reproduce pass/fail results for package-testing workflows distinct from unit tests to establish.
    0 installs
20. ▌
    Gnps Workflow Identification 2 · holobiomicslab

    Use when you have downloaded a GNPS molecular networking job archive and need to extract its contents (spectra.mgf, molecular_families.tsv, annotations.tsv, file_mappings) but do not know which GNPS workflow version produced it, preventing correct file naming and downstream computational analysis.
    0 installs
21. ▌
    Heatmap Visualization Design 2 · holobiomicslab

    Use when after training a DeepMSProfiler model and generating per-sample predictions: when you need to display Pearson or Spearman correlation coefficients between individual metabolite signals and disease class labels in a matrix form suitable for publication or exploratory review of.
    0 installs
22. ▌
    Homologous Series Clustering 2 · holobiomicslab

    Use when you have a feature list (m/z, retention time, intensity) from HRMS data and want to identify potential PFAS homologous series for prioritization.
    0 installs
23. ▌
    HTTP API Integration Testing 2 · holobiomicslab

    Use when you have deployed a microservice (e.g., TensorFlow Serving, REST API) and need to verify that specific endpoints (e.g., /model/metadata, /classify) return responses with correct schema, field names, and data types before consuming them in production workflows or downstream applications.
    0 installs
24. ▌
    HTTP Endpoint Identification 2 · holobiomicslab

    Use when when you have source code access to a webservice component (such as the MAGMa joblauncher) and need to enumerate all exposed HTTP endpoints, their methods (GET, POST, etc.), URL patterns, parameter names, request/response payload structures, and authentication requirements in order to.
    0 installs
25. ▌
    Intensity Frequency Analysis 2 · holobiomicslab

    Use when you have an MS/MS peak list and need to remove electronic noise—specifically when you observe suspiciously identical intensity values repeated across multiple peaks in a single spectrum, which is characteristic of instrument-generated artifacts rather than genuine analyte signals.
    0 installs
26. ▌
    Isotopic Impurity Accounting 3 · holobiomicslab

    Use when when analyzing LC-MS data from stable isotope labeling experiments where measured isotopologue abundances are contaminated by naturally occurring isotopes and tracer isotopic impurity, and you have access to unlabeled sample reference measurements to empirically model these confounding.
    0 installs
27. ▌
    Knime Workflow Orchestration 3 · holobiomicslab

    Use when you have raw LC-MS data (mzML, NetCDF) from multiple runs that require sequential feature detection, alignment, quantification, and optional filtering (e.g., blank exclusion, QC reproducibility, retention-time outlier removal) before spatial mapping or annotation.
    0 installs
28. ▌
    Lipid Identification Scoring 3 · holobiomicslab

    Use when after peak picking (MZmine, XCMS, MS-DIAL, or Compound Discoverer output) and candidate retrieval, when you have experimental fragment m/z values and multiple candidate lipid species from the in-silico library.
    0 installs
29. ▌
    Lipid Species Identification 2 · holobiomicslab

    Use when you have centroid-mode LC–MS AIF chromatograms processed by xcms and RamClustR (or equivalent), a feature table with m/z and retention time coordinates, and you need to resolve individual lipid species identities with confidence scores and fragmentation evidence.
    0 installs
30. ▌
    Mandatory Field Verification 2 · holobiomicslab

    Use when after generating mzPeak files from prototype implementations (Rust, Python, R, or .NET) or after format conversion, and before integrating files into a mass spectrometry data repository or sharing them with collaborators. Use it when specification compliance is a hard requirement (e.
    0 installs
31. ▌
    Massql Query Language Syntax 2 · holobiomicslab

    Use when you need to search for specific mass spectrometry patterns (e.g., precursor ion m/z, product ion presence, retention time windows, intensity constraints, neutral loss patterns) across one or more mzML files.
    0 installs
32. ▌
    Matplotlib Heatmap Rendering 2 · holobiomicslab

    Use when when you have a confusion matrix (predicted vs. ground-truth labels) or similarity matrix (pairwise scores between spectra) and need to communicate classification accuracy or chemical similarity patterns through a visual heatmap.
    0 installs
33. ▌
    Metabolite Candidate Ranking 2 · holobiomicslab

    Use when you have an untargeted mass spectrometry spectrum (MS/MS data) and a set of candidate molecules from PubChem or similar databases, and you need to rank candidates by likelihood of being the true molecular annotation.
    0 installs
34. ▌
    Metabolite Database Matching 2 · holobiomicslab

    Use when after peak networks have been identified and clustered from INADEQUATE spectra (typically via the clustering and finding modules), use this skill when you need to assign chemical identities to unknown peak networks by comparing them against reference spectral signatures in a simulated.
    0 installs
35. ▌
    Metabolite Ion Consolidation 2 · holobiomicslab

    Use when after chromatographic peak detection in LC-MS data, when you have hundreds or thousands of features and need to consolidate ions presumed to originate from the same metabolite.
    0 installs
36. ▌
    Metabolomic Feature Matching 2 · holobiomicslab

    Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) from separate metabolomic experiments or replicates, and you need to establish which features in dataset A correspond to which features in dataset B to enable comparative or longitudinal analysis.
    0 installs
37. ▌
    Metabolomics Data Formatting 2 · holobiomicslab

    Use when after running feature clustering (Gravity) or drift correction (Blueshift) on LCMS data, when you have a processed feature table and need to standardize its structure, validate metadata completeness, enforce missing-value thresholds, and generate a QC report documenting pass/fail status.
    0 installs
38. ▌
    Metabolomics Ora Methodology 2 · holobiomicslab

    Use when you have a metabolomics dataset and want to perform pathway enrichment analysis using ORA, but need to first understand its behavior, limitations, and correct application through reproducible simulation.
    0 installs
39. ▌
    Metabolomics Tool Deployment 3 · holobiomicslab

    Use when you have a Galaxy installation (specifically Galaxy Master branch commit c429777c93680dcee449fe410f5360afbe673758 or compatible) and need to add metabolomics analysis capabilities including tools for XCMS integration, mass spectrometry file reading (via MSFileReader), and metabolite.
    0 installs
40. ▌
    Metadata Coldata Integration 2 · holobiomicslab

    Use when when you have generated a feature abundance matrix from mzrtsim() peak list simulation with known sample-level attributes (condition assignments, batch labels, sample identifiers) and need to package this into a SummarizedExperiment object for Bioconductor-compatible analysis pipelines.
    0 installs
41. ▌
    Metadata Field Normalization 2 · holobiomicslab

    Use when immediately after importing raw mass spectrometry data from mzML, mzXML, msp, MGF, or JSON formats into matchms.
    0 installs
42. ▌
    Model Checkpoint Persistence 2 · holobiomicslab

    Use when training a Transformer or neural network model on a large dataset (e.g., 80,000+ training samples) where validation performance is monitored to prevent overfitting, and you need to halt training early or recover the -performing model checkpoint without re-executing the entire training loop.
    0 installs
43. ▌
    Model Deployment Preparation 2 · holobiomicslab

    Use when you have a pre-trained Keras model and need to deploy it via a Docker-based TensorFlow Serving API (e.g., for molecular classification via SMILES), but the model's layer naming or format does not yet match the target runtime's expectations (e.
    0 installs
44. ▌
    Molecular Formula Assignment 2 · holobiomicslab

    Use when you have acquired MS/MS spectra (in MGF format with required fields: TITLE, PRECURSOR_MZ, PRECURSOR_TYPE, COLLISION_ENERGY) from known or unknown compounds and need to predict their molecular formulas with ranked candidates and confidence scores.
    0 installs
45. ▌
    Molecular Formula Prediction 2 · holobiomicslab

    Use when you have 1D ¹H or ¹³C NMR spectra from an unknown organic compound and need to predict its molecular formula (e.g., C₆H₁₂O₂). The compound must contain ≤19 heavy (non-hydrogen) atoms. Use this as the first stage of a structure elucidation pipeline before predicting molecular connectivity.
    0 installs
46. ▌
    Ms Feature Tree Construction 2 · holobiomicslab

    Use when you have untargeted LC-MS/MS metabolomic data (peak-detected .mzXML/.mzML/.mzDATA files processed through MZmine2) and need to relate MS1 features by chemical similarity rather than sequence homology.
    0 installs
47. ▌
    Ms Spectral Library Matching 2 · holobiomicslab

    Use when when you have a GC-MS dataset (CSV with columns: Component.RT, Component.Area, Base.Peak.MZ, File.Name, Compound.Name, Match.Factor) and a known set of target chemicals you wish to locate and extract with their spectral match quality and quantitation.
    1 install
48. ▌
    Msconvert Tool Configuration 2 · holobiomicslab

    Use when you have vendor-specific raw mass spectrometry data files (e.g., from Orbitrap, Q-TOF, or other MS instruments) and need to feed them into IsoFusion or other tools that require MS1 format as input.
    0 installs
49. ▌
    Msp File Parsing And Writing 2 · holobiomicslab

    Use when you have one or more .msp spectral library files (NIST format) that need to be ingested for metadata curation, enrichment via web services, or export after transformation. Use this skill as the entry and exit point for any .msp-based annotation or analysis pipeline.
    0 installs
50. ▌
    Multi Class Label Assignment 2 · holobiomicslab

    Use when you have raw LC-MS metabolomics data from multiple disease groups and need to classify new or existing samples into discrete disease categories.
    0 installs
51. ▌
    Mzml Data Access Abstraction 2 · holobiomicslab

    Use when when building or extending a mass spectrometry data parser that must support multiple mzML storage formats (plain .mzML, indexed .mzML.gz, standard-compressed .mzML.
    0 installs
52. ▌
    Mzml Spectral Format Parsing 2 · holobiomicslab

    Use when you have mzML-format raw data files (from any mass spectrometry vendor or conversion tool) and need to ingest them into MS-DIAL version 5 or later for untargeted metabolomics or lipidomics analysis.
    0 installs
53. ▌
    Noise Level Parameter Tuning 3 · holobiomicslab

    Use when when you have an aligned GCIMS dataset and need to configure the findPeaks function with CWT algorithm to detect peaks across retention time and drift time dimensions.
    0 installs
54. ▌
    Pairwise Spectrum Comparison 2 · holobiomicslab

    Use when you have a collection of cleaned mass spectrometry spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to identify spectral similarities, find related compounds, or generate a comprehensive similarity matrix for downstream analysis such as spectral library matching or clustering.
    0 installs
55. ▌
    Pareto Scaling Normalization 2 · holobiomicslab

    Use when you have peak intensity vectors from LC/GC-MS experiments with corresponding QC (quality control) sample measurements, and you need to correct for batch effects—especially when QC samples show systematic shifts in peak heights across analytical batches.
    0 installs
56. ▌
    Peak Abundance Normalization 2 · holobiomicslab

    Use when after peak detection and before any comparative analysis (e.g., diversity indices, ordination, or statistical testing) when working with direct injection FT-ICR MS data where raw peak intensities vary across samples due to instrumental factors. The task_id=task_005 example applies it to S.
    0 installs
57. ▌
    Peak Intensity Normalization 2 · holobiomicslab

    Use when you have raw MS/MS spectral peak lists with absolute intensity values and need to compare spectra using entropy similarity, dot product, or other distance metrics.
    0 installs
58. ▌
    Peak Recovery Post Filtering 2 · holobiomicslab

    Use when after applying cluster-based filtering with quasi-molecular adduct constraints and frequency thresholds on LC-MS feature candidates, when some peaks have been entirely removed from the candidate pool and you want to prevent loss of true metabolites that failed to meet filtering criteria.
    0 installs
59. ▌
    Peak Table Schema Validation 2 · holobiomicslab

    Use when after converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format. Use this skill when you need to verify that the converted file will be successfully read by LipidMatch before proceeding to lipid identification;
    0 installs
60. ▌
    Proforma Peptidoform Parsing 2 · holobiomicslab

    Use when when you have a ProForma 2.0–formatted peptide string with PSI-MOD or UniMod modification labels and need to extract the underlying amino acid sequence and modification positions before performing theoretical fragment ion calculation or spectrum peak matching.
    0 installs
61. ▌
    Project Metadata Integration 2 · holobiomicslab

    Use when a paired omics project record contains a genome identifier (e.g., GenBank accession) but lacks the corresponding organism name field, and you need to populate that metadata field to enable full text search, sample tracking, or project validation before archival to Zenodo.
    0 installs
62. ▌
    Pull Request Change Tracking 2 · holobiomicslab

    Use when investigating how a specific pull request (e.g., PR #72 introducing MS2Query's two-branch workflow split) modified the codebase architecture, control flow, or data routing.
    0 installs
63. ▌
    Pytorch Model Implementation 2 · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (m/z and intensity arrays) and need to map it to a fixed-size latent vector for use in an encoder–decoder architecture. Specifically applicable when the downstream task requires a molecular structure reconstruction (e.
    0 installs
64. ▌
    Qcpool Sample Identification 2 · holobiomicslab

    Use when you have Sciex Multiquant (≥v3.0.3) TXT export files containing metabolomics or lipidomics analytical sequences that include pooled QC samples, and you need to verify that QCpool samples were injected at the designed regular intervals and extract their positional metadata for quality.
    0 installs
65. ▌
    Repository Cloning And Setup 2 · holobiomicslab

    Use when when you need to deploy a containerized scientific tool (e.g., CloMet) for the first time on a local machine or CI/CD environment, and the project provides a Dockerfile and GitHub repository.
    0 installs
66. ▌
    Repository Source Code Setup 2 · holobiomicslab

    Use when you need to validate that a published software tool (e.g., MassQL) executes correctly in your environment, reproduce published results, or contribute to development.
    0 installs
67. ▌
    Repository Structure Parsing 2 · holobiomicslab

    Use when when you encounter a multi-module scientific software project (e.
    0 installs
68. ▌
    Retention Time Peak Flagging 2 · holobiomicslab

    Use when after applying peak detection algorithms to identify local maxima in feature signals across retention time or m/z dimensions, but before exporting or filtering the peak list for further analysis.
    0 installs
69. ▌
    Sample Missingness Filtering 2 · holobiomicslab

    Use when when you have loaded (un)targeted metabolite data into a Metaboprep object and need to exclude samples with excessive missing values before quality control or statistical analysis. This is typically applied early in the QC pipeline when sample-level data completeness is a concern (e.
    0 installs
70. ▌
    Similarity Matrix Generation 2 · holobiomicslab

    Use when you have a collection of cleaned spectra in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compute all pairwise similarity scores to identify related or duplicate spectra, support spectral library searching, or enable network-based analysis.
    0 installs
71. ▌
    Similarity Score Computation 2 · holobiomicslab

    Use when when you have a query electron ionization mass spectrum (m/z and intensity pairs) and need to identify the most similar spectra from an MSP-formatted spectral library.
    0 installs
72. ▌
    Spectral Entropy Calculation 2 · holobiomicslab

    Use when when you have preprocessed MS/MS spectral peak data (m/z and intensity pairs) and need to compute a complexity metric for individual spectra prior to similarity comparisons, or when benchmarking compound identification performance against dot product–based methods.
    0 installs
73. ▌
    Spectral File Format Parsing 2 · holobiomicslab

    Use when you receive raw spectral data files (jcamp, RAW, or mzML) from NMR, IR, or MS instruments and need to extract peak tables, metadata, and spectral parameters before generating visualizations, performing peak annotation, or converting to standardized output formats.
    0 installs
74. ▌
    Spectral Fragment Assignment 2 · holobiomicslab

    Use when when you have an experimental tandem mass spectrum (peaks with m/z and intensity values) and wish to identify which fragments or chemical subformulae each peak corresponds to.
    0 installs
75. ▌
    Spectral Metadata Enrichment 2 · holobiomicslab

    Use when you have a .msp spectral library file with sparse or incomplete metadata (e.
    0 installs
76. ▌
    Spectral Metadata Extraction 2 · holobiomicslab

    Use when after loading an MSP spectral library file into memory using mssearchr's MSP parser, when you need to verify that each spectrum record contains complete and valid metadata (precursor m/z values, peak lists, header annotations) before writing the parsed spectra to a new MSP file or.
    0 installs
77. ▌
    Spectral Peak Shape Modeling 3 · holobiomicslab

    Use when when generating synthetic LC/GC-MS .mzML files from MoNA or HMDB spectral records where you need to compute absolute ground-truth maximum intensity (sim_ins) for each peak while accounting for chromatographic band broadening, peak tailing, and retention-time dispersion.
    4 installs
78. ▌
    Spectral Similarity Grouping 2 · holobiomicslab

    Use when when you have computed a sparse pairwise distance matrix from nearest neighbor indexes of high-resolution MS/MS spectra and need to partition them into clusters such that spectra within each cluster correspond to similar fragmentation patterns (e.g., same peptide or metabolite).
    0 installs
79. ▌
    Structured Report Generation 2 · holobiomicslab

    Use when after applying jsonschema validation to a parsed mwTab file against MS or NMR schema definitions, when you have collected validation errors, warnings, and metadata column matching results and need to communicate findings to data curators or submitters in a structured, machine-readable.
    0 installs
80. ▌
    Structured Result Validation 2 · holobiomicslab

    Use when after retrieving a JSON or tabular response from a web service endpoint (such as CANOPUS), validate the result before parsing or integrating it into your analysis pipeline.
    0 installs
81. ▌
    Tandem Mass Spectrum Parsing 2 · holobiomicslab

    Use when when you have raw or instrument-native tandem mass spectrometry data (MS/MS) in formats such as mzML, mzXML, or proprietary binary formats, and you need to align, match, or compare spectra using methods like SIMILE that require structured access to precursor m/z, fragment m/z values, and.
    0 installs
82. ▌
    Tandem Ms Feature Assessment 2 · holobiomicslab

    Use when after importing raw peak tables from tandem MS/MS preprocessing software (e.
    0 installs
83. ▌
    Targeted Peak Extraction Ms1 3 · holobiomicslab

    Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a predefined list of molecular targets (CSV with m/z and/or retention time) that you need to quantify.
    0 installs
84. ▌
    Mass Shift Tolerance Scoring 2 · holobiomicslab

    Use when when searching for peptide spectra with unknown or open modifications (i.e., any mass shift within a broad tolerance range rather than a fixed set of known modifications).
    0 installs
85. ▌
    Mass Spectrum Plot Rendering 2 · holobiomicslab

    Use when after importing and preprocessing mass spectrometry data (in .raw, .
    0 installs
86. ▌
    Metabolic Ion Peak Filtering 2 · holobiomicslab

    Use when you have a raw or extracted peak feature table (CSV or tabular format) containing mass-to-charge ratios, retention times, and intensity values across multiple samples from different experimental groups, and you need to identify which peaks show statistically significant differential.
    0 installs
87. ▌
    Metabolomics Data Processing 2 · holobiomicslab

    Use when when you have raw or partially processed metabolomics data (feature tables with sample metadata) and need to apply quality-control metrics, normalization, statistical inference, or advanced classification/variable selection without relying on a Galaxy instance.
    0 installs
88. ▌
    Metabolomics Data Validation 2 · holobiomicslab

    Use when you have raw or semi-processed m/z peak lists (positive and negative ion mode) and a sample metadata table, and you need to confirm they meet MetaboShiny's structural and semantic requirements before loading them into the normalization pipeline.
    0 installs
89. ▌
    Package Metadata Compilation 2 · holobiomicslab

    Use when when a package README or publication claims to install a large, fixed number of tools (e.g., 'approximately 89 tools') but does not enumerate them explicitly.
    0 installs
90. ▌
    Raw File Routing And Queuing 2 · holobiomicslab

    Use when you have collected raw MS files via an uploader tool and need to automatically forward them to a data processor for proteomics analysis, ensuring format compatibility and maintaining linkage to the original upload session and user project.
    0 installs
91. ▌
    Search Engine Output Parsing 2 · holobiomicslab

    Use when you have PSM output files from one or more search engines (e.g., MaxQuant msms.txt, MSGFPlus .mzid, Sage .sage.
    0 installs
92. ▌
    Taxonomy Metadata Extraction 2 · holobiomicslab

    Use when you have executed a spectrum search against one or more domain-specific MASSTs (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, or foodMASST) and need to systematically extract taxonomic lineages (kingdom, phylum, class, order, family, genus, species, strain) and sample metadata.
    0 installs
93. ▌
    Tic Peak Boundary Estimation 2 · holobiomicslab

    Use when after sliding-window analysis has identified candidate TIC peaks but before parameter extraction from Extracted Ion Chromatograms (EICs).
    0 installs
94. ▌
    Tool XML Wrapper Integration 2 · holobiomicslab

    Use when you have standalone metabolomics analysis tools (Python scripts, R packages, MATLAB compiled applications) that you want to expose through Galaxy's UI and make composable into reproducible workflows.
    0 installs
95. ▌
    Deep Learning Model Training 2 · holobiomicslab

    Use when you have raw or preprocessed mass spectrometry feature matrices (e.g., from low mass resolution or sparse acquisition) and want to enhance signal quality and spatial resolution across tissue or single-cell samples.
    0 installs
96. ▌
    Spectral Baseline Correction 2 · holobiomicslab

    Use when you have loaded raw MSI spectral data (imzML format) in profile or centroid mode and need to remove background noise and baseline artifacts before intensity normalization or ROI analysis.
    0 installs
97. ▌
    Spectral Noise Reduction Msi 2 · holobiomicslab

    Use when you have imported raw MSI spectral data in imzML format and observe high background noise or low signal-to-noise ratio that would obscure biochemical annotations or ROI analysis.
    0 installs
98. ▌
    Blank Intensity Ratio Filtering 2 · holobiomicslab

    Use when apply this filter after feature detection and before downstream statistical analysis when your experimental design includes blank samples (e.
    0 installs
99. ▌
    Centroided Ms Feature Detection 3 · holobiomicslab

    Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass, chromatographic, and intensity dimensions as input to PFAS prioritization, suspect screening, or other MS-based analyses.
    0 installs
100. ▌
     Feature Grouping By Mass Defect 2 · holobiomicslab

     Use when you have a feature list with m/z values from HRMS data and need to identify homologous PFAS series to prioritize suspect screening.
     0 installs