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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Color Jitter Application Imaging · holobiomicslab

   Use when preparing ion image data for representation learning in mass spectrometry imaging, specifically when you need to augment raw ion images to generate pairs of diverse views for contrastive loss training.
   0 installs
2. ▌
   Community Constraint Propagation · holobiomicslab

   Use when you have consensus metabolic reconstructions for multiple community members (e.g., from a plant microbiome or synthetic consortium) and need to gap-fill incomplete models while preserving community-level feasibility.
   0 installs
3. ▌
   Converter Architecture Traversal · holobiomicslab

   Use when when you need to understand which chemical identifier conversions are available in MSMetaEnhancer (e.
   0 installs
4. ▌
   Cpu Gpu Performance Benchmarking · holobiomicslab

   Use when you have implemented both CPU and GPU versions of a spectral search algorithm (e.g., approximate nearest neighbor indexing with cascade filtering) and need to validate whether GPU acceleration is justified.
   0 installs
5. ▌
   Cyp Isoform Substrate Prediction · holobiomicslab

   Use when you have a set of molecular structures (in .sdf or .csv SMILES format) and need to predict which CYP isoforms will metabolize them.
   0 installs
6. ▌
   Cyp450 Enzyme List Specification · holobiomicslab

   Use when when you need to predict drug or xenobiotic metabolites across multiple CYP450 isoforms and must communicate which specific enzymes (e.g., 1A2, 2C9, 3A4) should be evaluated. Use this skill before invoking a metabolite prediction tool that accepts an enzyme list parameter.
   0 installs
7. ▌
   Cypreact Input Format Compliance · holobiomicslab

   Use when you have a collection of molecular structures intended for CypReact-based CYP isoform metabolism prediction and need to verify the input file conforms to CypReact's expected format (comma-separated SMILES in .csv or SDF molecular structure files) before submission to the tool.
   0 installs
8. ▌
   Database Integration And Linkage · holobiomicslab

   Use when you have a list of metabolite identifiers sourced from one metabolome database (e.g., HMDB IDs, PubChem CIDs) and need to map them to equivalent identifiers in other databases for data integration, cross-referencing, or standardization in downstream metabolomics analysis.
   0 installs
9. ▌
   Dependency Version Specification · holobiomicslab

   Use when you encounter a scientific implementation (particularly deep learning or complex data processing pipelines) where the original authors have documented specific software versions, and you need to reproduce the exact computational environment.
   0 installs
10. ▌
    Docker Container Volume Mounting · holobiomicslab

    Use when when you have vendor raw mass spectrometry files on the host machine that need to be processed by a containerized tool (e.g., AirdPro), and the container must read input from and write output to specific host paths. Typical trigger: you have a .
    0 installs
11. ▌
    Dockerfile Dependency Management · holobiomicslab

    Use when when deploying a Shiny application with mixed R and Python dependencies (e.g., pmartR backend with Kaleido for plot export) to production or CI/CD pipelines, and when some dependencies are under active development alongside the application.
    0 installs
12. ▌
    Domain Specific Language Parsing · holobiomicslab

    Use when when you have SQL-inspired query strings that encode domain-specific assumptions and need to validate, transform, or execute them against data repositories. Specifically: input is human-readable DSL text containing mass spectrometry-specific clauses (e.
    0 installs
13. ▌
    Elemental Composition Extraction · holobiomicslab

    Use when you have formula-assigned FT-ICR MS data (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify elemental stoichiometry, compute diversity indices, or assess molecular complexity across environmental organic mixtures.
    0 installs
14. ▌
    Expression Matrix Transformation · holobiomicslab

    Use when you have loaded raw expression data (linear-scale peptide or protein abundance quantification) into pmartR and need to prepare it for statistical analysis.
    0 installs
15. ▌
    Fdr Aware Psm Retention Strategy · holobiomicslab

    Use when rescoring PSMs with machine learning or statistical models where: (1) you want to consider multiple candidate PSMs per spectrum (e.
    0 installs
16. ▌
    Feature Vector Naming Convention · holobiomicslab

    Use when when applying sequential transformations to a metabolomics feature intensity table (samples × compounds) and you need to maintain a traceable record of original feature identities through each processing stage.
    0 installs
17. ▌
    Fixed Effect Regression Analysis · holobiomicslab

    Use when you have a long-format metabolomics dataset with one row per observation and need to estimate the independent association between one or more fixed effects (e.g., exposure dose, treatment group, demographic variable) and each dependent variable (e.
    0 installs
18. ▌
    Gene Network Seed Initialization · holobiomicslab

    Use when when you have metabolomic enrichment scores for genes (e.g., from MSEA analysis comparing a patient to controls) and need to prepare them as seed labels for label propagation over a gene/protein interaction network.
    0 installs
19. ▌
    Gene Tokenization Representation · holobiomicslab

    Use when when you have GenBank-format BGC sequences with Pfam domain annotations and need to prepare them for sub-cluster detection, redundancy filtering, or natural product structure association.
    0 installs
20. ▌
    Genomic Bgc Extraction Antismash · holobiomicslab

    Use when when you have genomic DNA sequences (from isolates or metagenomes) and need to identify and characterize biosynthetic gene clusters as input for downstream natural product linkage analysis.
    0 installs
21. ▌
    Graph Neural Network Fine Tuning · holobiomicslab

    Use when when you have a pre-trained GNN checkpoint and a smaller, task-specific dataset (e.g., Eawag_XBridgeC18_364.
    0 installs
22. ▌
    HTML Bundle Rendering In Browser · holobiomicslab

    Use when you have a dashboard_data.json file (JSON export from the msFeaST pipeline) and need to interactively explore quantification tables, metadata, and spectral data on a desktop machine (macOS, Linux, or Windows).
    0 installs
23. ▌
    Hyperdimensional Vector Encoding · holobiomicslab

    Use when you have preprocessed mass spectra (mz/intensity pairs in MGF format) and need to convert them into a compact, fixed-dimensional representation suitable for fast similarity computation and clustering.
    0 installs
24. ▌
    Image Threshold Method Selection · holobiomicslab

    Use when you have loaded a laser ablation ICP-MS image into pewpew and need to separate tissue pixels from background regions to enable region-based analysis or quantification.
    0 installs
25. ▌
    Interactive Plot Rendering Bokeh · 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
26. ▌
    Ion Mobility Feature Engineering · holobiomicslab

    Use when you have a set of metabolite structures (or their molecular descriptors) and need to construct training or target feature matrices for CCS prediction. Specifically, use it when you are preparing data to fit or apply a machine learning model (e.g., Sklearn v1.0.
    0 installs
27. ▌
    Jacobian Matrix Graph Conversion · holobiomicslab

    Use when after computing a Jacobian matrix from covariance data in MInfer, when you need to visualize and interpret the structure of metabolite-to-metabolite interactions as a network.
    0 installs
28. ▌
    Lipid Class Abundance Comparison · holobiomicslab

    Use when you have a LipidomicsExperiment object with logged and normalized Area measurements, sample-level phenotype annotations (e.g., SampleType: Cancer, Benign, Metastasis), and you want to identify which lipid classes show consistent directional change across all samples within a group.
    0 installs
29. ▌
    Loess Smoothing Parameter Tuning · holobiomicslab

    Use when your metabolomics SummarizedExperiment object shows signal drift across replicate measurements within individual batches (visible as systematic trends in PCA plots or replicate scatter), and you have intra-batch replicate samples available to estimate smooth drift corrections.
    0 installs
30. ▌
    M Z Intensity Feature Extraction · holobiomicslab

    Use when you have imported mass spectrometry data in .raw, .d, or mzXML format and need to inspect peak structure, verify instrument performance, or generate baseline visualizations before downstream peak annotation or statistical analysis.
    0 installs
31. ▌
    M Z Window Tolerance Application · holobiomicslab

    Use when after parsing an imzML XML metadata file and loading the corresponding .ibd binary intensity data, when you need to isolate and visualize the spatial distribution of specific isotopes, chemical species, or mass fragments.
    0 installs
32. ▌
    Marker Ion Ranking And Filtering · holobiomicslab

    Use when you have extracted latent low-dimensional peak features from imaging mass spectrometry (IMS) data using a graph-attention autoencoder and need to identify a ranked subset of marker ions that represent spatial metabolomic patterns.
    0 installs
33. ▌
    Mass Error Distribution Analysis · holobiomicslab

    Use when after applying polynomial m/z recalibration using a reference peak list (e.g., SRFA.ref) to an FT-ICR mass spectrum.
    0 installs
34. ▌
    Mass Error Threshold Calibration · holobiomicslab

    Use when you have isolated TIC peak regions and need to extract ion chromatograms (EICs) for XCMS parameter estimation via the EICparams function. Use it specifically when your mass analyzer's measurement accuracy is known (e.
    0 installs
35. ▌
    Mass Spectrometry Format Parsing · holobiomicslab

    Use when you have mzML or mzXML mass spectrometry data files and need to extract and validate spectral records (m/z and intensity arrays) for lossless compression, lossy transformation, or format conversion.
    0 installs
36. ▌
    Mass Spectrometry Quantification · holobiomicslab

    Use when you have measured MS intensity data from unknown samples and known-concentration standard compounds, and you need to convert sample intensities into predicted concentrations. Specifically applicable when intensity drift is observed across the measurement sequence (e.
    0 installs
37. ▌
    Metabolic Network Reconstruction · holobiomicslab

    Use when you have matched multiomics data (genomics, epigenomics, transcriptomics, proteomics, metabolomics) across a cohort of cell lines or samples and want to infer which molecular features (genes, transcripts, proteins, methylation sites) regulate metabolite abundance.
    0 installs
38. ▌
    Metabolite Annotation Validation · holobiomicslab

    Use when after running in silico annotation tools (SIRIUS, ISDB) or spectral library matching on your feature table, when you need to retain only annotations meeting a minimum confidence threshold.
    0 installs
39. ▌
    Metabolite Binary Classification · holobiomicslab

    Use when you have a preprocessed metabolomics dataset with a binary outcome variable (e.
    0 installs
40. ▌
    Metabolite Output Interpretation · holobiomicslab

    Use when after running CyProduct with a query molecule (SMILES or SDF) and a list of CYP450 enzymes, use this skill to collect, organize, and validate the predicted metabolite results stored in the output folder.
    0 installs
41. ▌
    Missing Value Imputation For Pca · holobiomicslab

    Use when your metabolomic dataset contains missing values (common in untargeted or targeted mass spectrometry data) and you need to perform PCA for outlier detection at multiple standard deviation thresholds (e.g., 3 SD, 4 SD, 5 SD) on principal component scores.
    0 installs
42. ▌
    Modification Label Normalization · holobiomicslab

    Use when when PSM files from heterogeneous proteomics search engines (MaxQuant, MSGFPlus, Sage, X!Tandem, etc.) use inconsistent or proprietary modification notations that cannot be directly consumed by feature generators (e.
    0 installs
43. ▌
    Molecular Descriptor Computation · holobiomicslab

    Use when when you have a query mass spectrum and a set of candidate molecular structures (as SMILES or 2D/3D coordinates), and you need to prepare them for cross-view similarity comparison or machine learning-based ranking.
    0 installs
44. ▌
    Molecular Structure File Parsing · holobiomicslab

    Use when when you have received or downloaded an SDF-formatted compound database file and need to verify that it is valid, uncorrupted, and contains the expected number of distinct molecular records before using it in metabolomics, cheminformatics, or toxicology workflows.
    0 installs
45. ▌
    Ms Instrument Data Preprocessing · holobiomicslab

    Use when you have raw mass spectrometry data files from a mass spectrometer instrument and need to feed them into a peptide feature detection pipeline (e.g., IsoFusion) that accepts only MS1 format input.
    0 installs
46. ▌
    Msconvert Workflow Configuration · holobiomicslab

    Use when when you need to convert vendor-specific raw mass spectrometry files (.raw) to the open mzML format using imzML Writer, and msconvert is not yet installed or its location is not recognized by the system.
    0 installs
47. ▌
    Multi Modal Projection Alignment · holobiomicslab

    Use when you have a mass spectrum and a set of candidate molecular structures, and need to rank candidates by their likelihood of matching the query spectrum.
    0 installs
48. ▌
    Multiclass Data Batch Correction · holobiomicslab

    Use when your input is a raw or prepared multi-class metabolomic peak table (in ExpressionSet format or CSV) where samples belong to distinct biological classes, and you have either QC samples (quality control replicates) or internal standards (IS) to anchor batch correction.
    0 installs
49. ▌
    Multivariate Ordination Analysis · holobiomicslab

    Use when when you have normalized peak intensities from FT-ICR MS metabolomic data (or similar high-dimensional compositional data) grouped by experimental treatments (e.g., phage type, incubation time) and want to visualize whether sample groups cluster separately in reduced dimensionality.
    0 installs
50. ▌
    Ncbi Accession Cross Referencing · holobiomicslab

    Use when you have parsed a collection of sequence files with associated GenBank/RefSeq accession identifiers (typically from JSON metadata fields like cluster.
    0 installs
51. ▌
    Neural Network Module Validation · holobiomicslab

    Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).
    0 installs
52. ▌
    Normalization Quality Assessment · holobiomicslab

    Use when after completing intra-batch and inter-batch normalisation steps on a SummarizedExperiment object containing metabolomics assays. Use it to confirm that a normalisation method (e.
    0 installs
53. ▌
    Numerical Formula Implementation · holobiomicslab

    Use when a formula is documented in a system or article (e.g., resource allocation, sizing, or tuning guidance) but lacks executable validation, or you need to confirm the formula produces the documented expected output (e.g., an 8GB system should yield exactly 4 workers).
    0 installs
54. ▌
    Omics Data Formatting Validation · holobiomicslab

    Use when when preparing raw omics data (gene expression matrices, differential abundance tables, or other quantitative omics assays) paired with sample/group metadata for import into a visualization dashboard.
    0 installs
55. ▌
    Omics Network Feature Extraction · holobiomicslab

    Use when after you have built a network object (adjacency matrix, edge list, or correlation output) from omics data and need to quantitatively describe network properties beyond visualization.
    0 installs
56. ▌
    Package Entry Point Verification · holobiomicslab

    Use when you need to confirm that a Python package (especially one distributed via pip or conda) has been correctly configured with a console script entry point and that the CLI is callable from the system shell.
    0 installs
57. ▌
    Pathway Enrichment Visualization · holobiomicslab

    Use when after running ORA on a set of significant metabolite PubChemCIDs (e.g., features with q-value < 1e-9 from ANOVA) against a metabolic pathway database, and you need to identify and communicate which pathways are robustly enriched in your case.
    0 installs
58. ▌
    Peakmap Visualization Generation · holobiomicslab

    Use when you have mass spectrometry data loaded into a Pandas DataFrame with columns for m/z, retention time (or ion mobility), and intensity, and you need to visualize the complete 2D peak map landscape to identify co-eluting features, assess data quality, or explore retention time and.
    0 installs
59. ▌
    Poisson Noise Injection Spectral · holobiomicslab

    Use when augmenting mass spectrometry ion images for contrastive learning, specifically when you need to simulate the natural Poisson noise that arises from photon-counting detectors in mass spectrometry imaging experiments.
    0 installs
60. ▌
    Polarizability Tensor Extraction · holobiomicslab

    Use when after ASE-ANI has filtered conformers to remove high-energy geometries, and you need to compute electronic properties required for CCS prediction.
    0 installs
61. ▌
    Polypeptide Property Computation · holobiomicslab

    Use when you have one or more polypeptide sequences (from FASTA, CSV, or direct input) and need to compute monoisotopic mass, average mass, isotopic distribution, charge state, or isoelectric point for downstream proteomics analysis such as MS database matching, retention time prediction, or.
    0 installs
62. ▌
    Pre Analytical Variable Encoding · holobiomicslab

    Use when you have collected blood samples under specific pre-analytical conditions (known time delay before/after centrifugation in hours, processing temperature in °C, matrix type: EDTA plasma or serum) and need to query ALISTER's stability database to assess whether analyte measurements should be.
    0 installs
63. ▌
    Prima Gui Initialization Windows · holobiomicslab

    Use when you are developing a standalone Perl application for Windows that requires a graphical interface and depends on external command-line tools (e.g., Gnuplot for visualization).
    0 installs
64. ▌
    Proteomics Data Structure Design · holobiomicslab

    Use when when building a mass-spectrometry analysis pipeline that must support multiple vendor and open formats (mzML, mzXML, Thermo, Agilent, Bruker, etc.) and you need to shield downstream tools from format-specific parsing logic.
    0 installs
65. ▌
    Proteomics Output Record Parsing · holobiomicslab

    Use when after the Proteomics_Data_Processor tool has completed analysis of raw mass spectrometry files and returned structured output records.
    0 installs
66. ▌
    Pubchem Structure Lookup By Name · holobiomicslab

    Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).
    0 installs
67. ▌
    Python Package Environment Setup · holobiomicslab

    Use when when you have cloned a Python package repository and need to verify that the package installs correctly and its test suite passes locally. This is the prerequisite workflow before running pytest or code formatters like black on the package source.
    0 installs
68. ▌
    Pytorch Checkpoint Serialization · holobiomicslab

    Use when a PyTorch-based model (such as a graph neural network trained on molecular retention-time data) has completed training or reached convergence, and you need to preserve the model state for later inference, evaluation, or transfer learning on new datasets.
    0 installs
69. ▌
    Quality Control Sample Filtering · holobiomicslab

    Use when after building a SummarizedExperiment from metabolomics measurements but before batch correction and internal standard recommendation.
    0 installs
70. ▌
    Rolling Window Outlier Detection · holobiomicslab

    Use when raw LA-ICP-MS image data contains isolated spike artifacts—pixels with anomalously high or low intensities relative to their spatial neighborhood—that distort downstream quantification or visualization.
    0 installs
71. ▌
    Sample Replicate Pair Assessment · holobiomicslab

    Use when you have high-throughput replicate measurements (e.g., mass spectrometry metabolomics) on biological replicates and need to identify which sample pairs exhibit reproducible feature signals across a threshold (typically 75% reproducibility).
    0 installs
72. ▌
    Sampling Protocol Reconstruction · holobiomicslab

    Use when you have access to ALISTER's web app or codebase and need to understand, validate, or replicate the internal logic that maps (analyte, matrix, time-delay, temperature) tuples to stability assessments and protocol recommendations.
    0 installs
73. ▌
    Sequence Availability Assessment · holobiomicslab

    Use when you maintain or curate a specialized sequence repository (such as MIBiG) and need to identify which sequences in your local genbanks directory are not publicly available via NCBI GenBank/RefSeq databases.
    0 installs
74. ▌
    Seurat Assay Metadata Extraction · holobiomicslab

    Use when you have a SpaMTP Seurat object with a 'Spatial' assay containing metabolomics features (m/z values) and their associated metadata columns (e.
    0 installs
75. ▌
    Spatial Metabolomics Integration · holobiomicslab

    Use when when you have paired spatial metabolomics and spatial transcriptomics measurements from the same tissue samples and need to identify how metabolite distributions relate to gene expression patterns at aligned spatial coordinates.
    0 installs
76. ▌
    Spectral Data Integrity Checking · holobiomicslab

    Use when after converting mass-spectrometry data from an existing format (mzML, mzXML, or vendor-specific formats) into mzPeak using command-line tools or API calls.
    1 install
77. ▌
    Spot Level Intensity Aggregation · holobiomicslab

    Use when after loading spatial metabolomics data (from CSV, imzML, or merged positive/negative ion modes) into an AnnData object, and before filtering or alignment steps.
    0 installs
78. ▌
    Sra Data Retrieval And Ingestion · holobiomicslab

    Use when your analysis requires raw sequencing reads stored in NCBI SRA (identified by SRR, SRX, or SRP accessions) OR you have local FASTQ files organized in a directory structure.
    0 installs
79. ▌
    Statistical Significance Testing · holobiomicslab

    Use when when you have computed rank-based accuracy metrics (top-1, top-5, top-10 hit rates) for two or more competing methods on the same test dataset (e.g., Orbitrap spectra), and need to determine whether performance differences are genuine rather than noise.
    0 installs
80. ▌
    Statistical Simulation Execution · holobiomicslab

    Use when you have access to a published repository containing simulation scripts (e.
    0 installs
81. ▌
    Structure File Format Conversion · holobiomicslab

    Use when you have raw structure input from diverse external databases (e.
    0 installs
82. ▌
    Taxonomic Classification Merging · holobiomicslab

    Use when you have a GNPS DBResult file with spectral library matches that lack ClassyFire superclass, class, and subclass annotations, and you need to augment those matches with standardized chemical taxonomy for consensus classification or downstream analysis.
    0 installs
83. ▌
    Test Driven Database Development · holobiomicslab

    Use when when you have an existing tool or library with file-based storage (JSON, CSV, binary formats) that needs to support efficient querying across large datasets, and you want to migrate to a relational database without breaking existing functionality or performance expectations.
    0 installs
84. ▌
    Total Ion Current Quantification · holobiomicslab

    Use when you have loaded a mass spectrometry imaging pixel array (NumPy format) and need to correct for variations in total ion signal across pixels before generating ion images or ratio images.
    0 installs
85. ▌
    Variational Autoencoder Training · holobiomicslab

    Use when after preprocessing and normalizing joint ST/SM AnnData objects using joint_adata_sm_st and normalize_total_joint_adata_sm_st, when you need to align spatial transcriptomics and metabolomics data to a unified latent resolution for multi-omics integration and cross-modal spatial pattern.
    0 installs
86. ▌
    Visual Studio Project Management · holobiomicslab

    Use when when you have cloned a multi-framework .NET project (e.g., MsdialWorkbench using .NET Framework 4.7.2, .NET Core 3.1, and .NET 6) and need to set up the build environment in Visual Studio, restore dependencies, select a specific build configuration (e.
    0 installs
87. ▌
    Masst Repository Scale Search Workflow · holobiomicslab bundle

    Use when you have a spectrum or feature of interest and want to know where else it occurs across all public metabolomics data — query preparation, repository-scale fastMASST search, specialized microbe/plant/food MASST for ecological context, and co-occurrence analysis.
    0 installs
88. ▌
    Ms2lda Substructure Discovery Workflow · holobiomicslab bundle

    Use when you want to discover shared substructures (Mass2Motifs) across a corpus of MS2 spectra via LDA topic modeling — convert MS/MS spectra into a bag-of-fragments document corpus, run MS2LDA (Latent Dirichlet Allocation) to infer recurring fragmentation motifs, annotate motifs against MotifDB / Spec2Vec embeddings, and map motifs back onto molecular-network features for substructure-level annotation of an untargeted LC-MS/MS dataset.
    0 installs
89. ▌
    Isoform Usage Bias Correction · holobiomicslab

    Use when when performing gene-level differential expression analysis on RNA-seq data where samples may express different isoforms of the same gene at different relative abundances. Specifically: (1) you have transcript-level quantification (e.
    0 installs
90. ▌
    Matrix Equivalence Validation · holobiomicslab

    Use when you have generated gene-level count matrices via two methodologically distinct routes—e.
    0 installs
91. ▌
    Quantification Output Parsing · holobiomicslab

    Use when you have transcript-level quantification output files (e.g., quant.sf from salmon, abundance.
    0 installs
92. ▌
    Read Mapping Rate Calculation · holobiomicslab

    Use when when comparing mapping performance between two mapper implementations (e.g., C++ salmon vs. Rust salmon), validating that a bug fix or algorithmic change did not degrade sensitivity, or establishing baseline quantification quality on benchmark datasets with known characteristics.
    0 installs
93. ▌
    Sparse Matrix Format Handling · holobiomicslab

    Use when your input is an AnnData object with expression matrix X as a sparse scipy matrix or Dask-backed array, and you need to apply preprocessing functions (normalization, PCA, filtering) that could trigger eager materialization.
    0 installs
94. ▌
    Spatial Omics Dataset Loading · holobiomicslab

    Use when you have a spatial transcriptomics experiment (e.
    0 installs
95. ▌
    Splicing Matrix Normalization · holobiomicslab

    Use when you have transcript-level quantification (TPM or counts from Salmon/kallisto) and need to quantify the inclusion level of specific alternative splicing events (exon skipping, intron retention, alternative splice sites, etc.) in a form suitable for differential splicing analysis across.
    0 installs
96. ▌
    Biomolecular Class Label Assignment · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or databases).
    0 installs
97. ▌
    Breath Sample Feature Normalization · holobiomicslab

    Use when after peak recognition has identified significant m/z signals in individual breath samples and you need to aggregate features by sample identifier before aligning features across multiple samples.
    0 installs
98. ▌
    High Dimensional Signal Enhancement · holobiomicslab

    Use when when you have raw or preprocessed mass spectrometry imaging (MSI) data with limited spatial resolution, high noise, or incomplete molecular coverage, and you want to enhance signal fidelity to support multiscale tissue–single-cell mapping or brain biochemical profiling.
    0 installs
99. ▌
    Metabolite Library Entry Generation · holobiomicslab

    Use when you have an experimental MS/MS spectrum (from MassBank or your own acquisition) and need to create a standardized library entry with ranked fragment ions for use in MetaboAnnotatoR or other fragment-based annotation pipelines.
    0 installs
100. ▌
     Ms1 Composite Spectra Deconvolution · holobiomicslab

     Use when you have high-resolution MS1 data (mzXML, mzML, or netCDF format) from LC/HRMS analysis and need to deconvolve composite spectra into individual fragmentation patterns without DDA or DIA acquisition.
     0 installs