← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

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

1. ▌
   Package Installation Verification And Testing 2 · holobiomicslab

   Use when a Python package has been relocated to a new repository location, reorganized to conform to new organizational standards (e.g., metabolomics-cloud conventions), or its dependencies, metadata, or CI/CD workflows have been modified.
   0 installs
2. ▌
   Pairwise Alignment With Anchor Prioritization 2 · holobiomicslab

   Use when when processing LC-MS metabolomics datasets with 10 or fewer samples and requiring reproducible mass track alignment across the cohort.
   0 installs
3. ▌
   Smiles String Translation And Standardization 2 · holobiomicslab

   Use when you have raw SMILES strings from multiple external database sources (e.g., PubChem, ChEMBL, vendor databases) that need to be integrated into a unified structure registry. Indicators include: (1) raw SMILES table exists at a known interim input path (e.
   0 installs
4. ▌
   Transformer Input Representation Construction 2 · holobiomicslab

   Use when you have variable-length MS/MS peak lists (m/z arrays and intensity arrays) that must be fed into a transformer architecture for tasks like compound identification or spectral clustering.
   2 installs
5. ▌
   Untargeted Metabolomics Marker Identification 2 · holobiomicslab

   Use when when you have untargeted GC–MS or LC–MS data in the form of a two-dimensional m/z vs retention time map and need to identify marker features without conventional peak picking.
   0 installs
6. ▌
   Regression Performance Metric Computation 2 · holobiomicslab

   Use when after generating collision cross section predictions on a validation or test set using a trained graph neural network model, and you need to quantify prediction accuracy and compare against reported performance metrics in the literature or prior experimental runs.
   1 install
7. ▌
   Signal Noise Ratio Improvement Validation 2 · holobiomicslab

   Use when after executing multidimensional smoothing, spike removal, or saturation repair on raw TOF-MS or IM-MS data (.d format from Agilent MassHunter) to confirm that signal quality has improved.
   2 installs
8. ▌
   Deep Learning Model Training And Validation 2 · holobiomicslab

   Use when you have paired mass-spectrometry spectral data (m/z and intensity arrays) with known molecular fingerprints or InChIKeys, and need to train a supervised deep learning model to predict fingerprints for novel spectra.
   0 installs
9. ▌
   Laser Ablation Isotope Image Interpretation 2 · holobiomicslab

   Use when you have imported a raw LA-ICP-MS raster image (line-by-line, spot-wise, or ablation-time-aligned format) and need to isolate tissue regions from instrumental background or air before quantifying regional elemental abundance.
   0 installs
10. ▌
    Molecular Structure Representation Learning 2 · holobiomicslab

    Use when when you have paired mass spectra and molecular structure data and need to train a model that can bidirectionally map between experimental spectra and chemical structures.
    0 installs
11. ▌
    Structural Identifier Completeness Checking 2 · holobiomicslab

    Use when preprocessing open mass spectrometry libraries (OMSLs) or aggregated spectral datasets where structural identifiers are inconsistently populated.
    0 installs
12. ▌
    Ion Image Augmentation Contrastive Learning 2 · holobiomicslab

    Use when when you have preprocessed mass spectrometry ion images (single-channel 2D arrays or multi-channel spectral images) and need to train a self-supervised encoder to learn low-dimensional representations for downstream tasks such as co-localized ion discovery (COL mode) or isotope ion.
    0 installs
13. ▌
    Word2vec Model Inference Unknown Word Handling 2 · holobiomicslab

    Use when when applying a pre-trained Word2Vec model to mass spectra at inference time (e.g., library matching or molecular networking), especially when the query spectra may contain fragment peaks or neutral losses not represented in the model's training vocabulary.
    0 installs
14. ▌
    Chemical Structure Sanitization And Validation 2 · holobiomicslab

    Use when you have translated or raw SMILES strings from a chemical structure curation pipeline and need to remove invalid chemical structures, resolve sanitization errors (e.
    2 installs
15. ▌
    Chimeric Spectra Classification Model Training 2 · holobiomicslab

    Use when when your DDA-mode LC-MS/MS data exhibits chimeric spectra patterns that differ systematically from the reference training set used in DNMS2Purifier, or when you wish to optimize purification sensitivity/specificity for your particular instrument, ionization method, or sample matrix.
    2 installs
16. ▌
    Chromatographic Peak Quality Metric Evaluation 2 · holobiomicslab

    Use when when processing untargeted LC-MS metabolomics data with XCMS and need to identify low-quality peak integrations that may introduce noise or bias into subsequent compound identification and quantification.
    0 installs
17. ▌
    Confounder Adjustment Epidemiological Analysis 2 · holobiomicslab

    Use when when testing associations between metabolic features (from NMR or MS) and a phenotype of interest (e.g., BMI, disease status) in a cohort where age, gender, or clinical confounders are known to correlate with both the metabolite and phenotype.
    2 installs
18. ▌
    Contrastive Learning For Cross Modal Retrieval 2 · holobiomicslab

    Use when you have paired MS/MS spectra and molecular structures (SMILES or SDF format) and need to perform compound identification by retrieving the correct structure for an unknown spectrum.
    0 installs
19. ▌
    Domain Specific Spectrum Search Implementation 2 · holobiomicslab

    Use when you have acquired one or more tandem MS/MS spectra and need to identify metabolites against a reference library filtered by biological domain (e.
    2 installs
20. ▌
    Feature Annotation Via Isotope Adduct Grouping 2 · holobiomicslab

    Use when after peak detection and feature extraction have produced a composite feature table with m/z, retention time, and intensity values for individual samples.
    0 installs
21. ▌
    Fid To Frequency Domain Fourier Transformation 2 · holobiomicslab

    Use when after simulating and convolving individual metabolite multiplets with realistic lineshapes (Lorentzian or Gaussian) and combining them into a single time-domain FID array.
    1 install
22. ▌
    Ion Mobility Mass Spectrometry Data Processing 2 · holobiomicslab

    Use when you have IM-MS lipidomics samples spiked with U13C-labeled internal standards (e.
    2 installs
23. ▌
    Mass Spectrometry Peak Alignment Visualization 2 · holobiomicslab

    Use when when you have aligned peak data from molecular networking (with m/z, intensity, retention time, and alignment quality metrics across multiple spectra) and need to interactively explore peak alignments under multiple filtering criteria (intensity thresholds, alignment score cutoffs, peak.
    2 installs
24. ▌
    Metabolite Stability Assessment Across Cohorts 2 · holobiomicslab

    Use when you have uploaded a pre-analytical data table containing sample metadata, processing timestamps (pre- and post-centrifugation), and NMR metabolomic measurements for a cohort of peripheral blood samples (plasma/serum), and you need to quantify the magnitude and direction of metabolite.
    0 installs
25. ▌
    Molecular Identifier Completeness Verification 2 · holobiomicslab

    Use when during MSP, MGF, JSON, or CSV file parsing when standardizing mass spectra from heterogeneous open mass spectral libraries (OMSLs).
    0 installs
26. ▌
    Ms Ms Spectrum Tokenization And Representation 2 · holobiomicslab

    Use when when you have raw MS/MS spectra in MSP format (or similar) with m/z–intensity peak pairs and need to prepare them for neural embedding models that require fixed-size discrete token inputs. Applies before generating dense spectral embeddings for retrieval or similarity scoring tasks.
    0 installs
27. ▌
    Multiplexed Spectra Recovery And Deconvolution 2 · holobiomicslab

    Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired from a multiplexed (interleaved) ion mobility experiment, and you need to recover individual, demultiplexed frames to reconstruct conventional IM-MS spectra for downstream omics analysis.
    0 installs
28. ▌
    Nearest Neighbor Clustering By Mass Difference 2 · holobiomicslab

    Use when processing LC-MS metabolomics studies with >10 samples where sample count and memory constraints make pairwise mass alignment infeasible.
    0 installs
29. ▌
    Network Component Identification And Filtering 2 · holobiomicslab

    Use when you have a GNPS GraphML molecular network and need to isolate cohesive subsets of spectra (components) before analyzing which fragmentation patterns explain them.
    2 installs
30. ▌
    Representation Vector Dimensionality Reduction 2 · holobiomicslab

    Use when after obtaining 512-dimensional representation vectors from the Encoder module, when you need to compress these vectors for visualization, clustering, or downstream classification tasks on mass spectrometry imaging data while maintaining interpretability of ion relationships.
    0 installs
31. ▌
    Retention Time Regression Output Specification 2 · holobiomicslab

    Use when after initializing and executing a forward pass through a dual-branch RT-Transformer model (combining fingerprint and molecular graph inputs) on a batch of molecular samples, to verify that the output tensor conforms to the expected shape, data type, and numeric range for retention time.
    0 installs
32. ▌
    Selectivity Metric Computation Chromatographic 2 · holobiomicslab

    Use when after peak detection on composite mass tracks when you need to evaluate whether a detected peak represents a pure, interference-free signal on its m/z channel.
    0 installs
33. ▌
    Untargeted Metabolomics Feature Interpretation 2 · holobiomicslab

    Use when you have an untargeted metabolomics feature table (m/z values, retention times, p-values from statistical testing) and need to infer which metabolic pathways are active without performing metabolite identification.
    0 installs
34. ▌
    Workflow Orchestration And Parallelization 2 · holobiomicslab

    Use when when you have a multi-step computational chemistry or molecular modeling pipeline (3+ sequential or parallel stages) that must process many molecules, each requiring repeated tool invocations with different parameters, and you need reproducibility, fault tolerance, and the ability to.
    0 installs
35. ▌
    Mass Spectra Tokenization Unified Vocabulary 2 · holobiomicslab

    Use when when you have paired mass spectra and molecular structure data and need to train a unified model for structure elucidation. Use this skill at the data preparation stage before pretraining, when you want both modalities to share representational capacity rather than operate in isolation.
    0 installs
36. ▌
    Metabolomics Feature Detection And Alignment 2 · holobiomicslab

    Use when you have raw metabolomics mass spectrometry data in mzML or mzXML format and need to extract, align, and normalize metabolic features across multiple samples or conditions.
    0 installs
37. ▌
    Standardized Region Export For Deep Learning 2 · holobiomicslab

    Use when you have LC-HRMS profile-mode data with detected local maxima (from gradient-descent peak finding) and need to prepare them as input for a convolutional neural network trained to classify peaks vs. background signal or to estimate peak boundaries and centers.
    2 installs
38. ▌
    Feature Metadata Alignment Across Dimensions 2 · holobiomicslab

    Use when you have loaded a feature-by-pixel intensity matrix from an MSI HDF5 container and need to perform dimension-preserving corrections (e.
    0 installs
39. ▌
    Imaging Mass Spectrometry Ion Identification 2 · holobiomicslab

    Use when you have imaging mass spectrometry data from spatial metabolomics experiments and need to reduce the high-dimensional peak space to a ranked set of marker ions for downstream spatial analysis (e.g., tissue region annotation or biomarker discovery).
    1 install
40. ▌
    Mass Spectral Missing Word Fraction Computation 2 · holobiomicslab

    Use when when applying a pre-trained Spec2Vec Word2Vec model to new mass spectra (particularly those outside the model's training distribution), you need to assess whether peaks and neutral losses in query spectra have been seen during model training.
    0 installs
41. ▌
    Chromatographic Peak Detection And Segmentation 2 · holobiomicslab

    Use when you have raw LC-MS data (mzML or vendor format) and need to discover and characterize all chromatographic features present, without prior knowledge of target analytes.
    1 install
42. ▌
    Collision Cross Section Matching And Annotation 2 · holobiomicslab

    Use when when you have LC-IM-MS/MS data with measured collision cross section (CCS) values and m/z assignments, and you need to disambiguate sterol isomers (particularly N-Me derived unsaturated sterols) by matching against a curated database of predicted CCS values and MS/MS fragmentation patterns.
    2 installs
43. ▌
    Collision Energy Optimization For Fragmentation 2 · holobiomicslab

    Use when when you have N-Me derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict MS/MS fragmentation patterns with collision-energy-dependent m/z values and intensities for downstream CCS prediction or LC-IM-MS/MS library matching.
    0 installs
44. ▌
    Marker Feature Identification Chromatography Ms 2 · holobiomicslab

    Use when when processing raw chromatography–mass spectrometry data (GC–MS or LC–MS) as a 2D m/z vs retention time map and you need to identify and visualize marker features for analyte discrimination without relying on conventional peak picking.
    2 installs
45. ▌
    Mass Spectrometry Data Structure Interpretation 2 · holobiomicslab

    Use when you have converted multidimensional MS data (from Agilent .d, Bruker ion mobility .d, Thermo .
    0 installs
46. ▌
    Mass Track Construction From Centroided Spectra 2 · holobiomicslab

    Use when when you have centroided mzML files from LC-MS metabolomics and need to construct high-mass-resolution mass tracks for each sample before alignment. Apply this skill at the start of an untargeted metabolomics workflow, before building a cross-sample MassGrid.
    0 installs
47. ▌
    Metabolite Candidate Ranking Likelihood Scoring 2 · holobiomicslab

    Use when you have a query mass spectrum matched to multiple candidate metabolites (by accurate mass, database lookup, or spectral similarity), and you possess or can train a DNN model for retention time prediction on your target chromatographic method.
    0 installs
48. ▌
    Molecular Conformer Generation And Optimization 2 · holobiomicslab

    Use when you have SMILES strings or 2D molecular structures of N-Me derived unsaturated sterol lipids (or other C=C-containing molecules) and need to generate 3D conformational and electronic structure data as input to a machine-learning CCS prediction model.
    0 installs
49. ▌
    Molecular Duplicate Detection And Deduplication 2 · holobiomicslab

    Use when after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
    0 installs
50. ▌
    Molecular Network Construction For Metabolomics 2 · holobiomicslab

    Use when you have untargeted metabolomics data (e.g., LC-MS/MS spectra) and need to organize compounds by structural relatedness to enable structure discovery for unknown metabolites.
    2 installs
51. ▌
    Organism Specific Metabolism Pathway Assignment 2 · holobiomicslab

    Use when you have observed metabolites (from LC-MS/MS, chromatography, or spectroscopy) whose identities are unknown, and you wish to constrain the candidate pool by leveraging organism-specific metabolism predictions.
    0 installs
52. ▌
    Performance Metric Extraction From Publications 2 · holobiomicslab

    Use when you have identified a claim that one tool outperforms another (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms') in a research article's abstract or introduction, but the specific metrics and results table are not included in the introductory text.
    0 installs
53. ▌
    Transformer Encoder Architecture Implementation 2 · holobiomicslab

    Use when when processing sequential spectroscopic data (1H NMR spectra) where both local chemical shift patterns and global spectral dependencies are needed for compound classification.
    0 installs
54. ▌
    Untargeted Metabolomics Workflow Implementation 2 · holobiomicslab

    Use when you have LC-MS/MS data acquired in DDA mode from untargeted metabolomics experiments and need to remove chimeric (co-fragmented) MS/MS spectra that result from multiple precursor ions fragmented simultaneously.
    0 installs
55. ▌
    Composite Mass Track Summation Across Samples 2 · holobiomicslab

    Use when after mass tracks have been aligned across samples into a MassGrid structure (m/z-aligned, same mass-to-charge ratio) and retention time calibration dictionaries have been computed for each sample.
    0 installs
56. ▌
    Molecular Fingerprint Representation Learning 2 · holobiomicslab

    Use when when you have labeled mass-spectrometry spectral data (precursor m/z and fragment m/z–intensity pairs) paired with known molecular structures (as InChIKeys or SMILES), and need to perform metabolite annotation by ranking candidate compounds based on spectral similarity.
    0 installs
57. ▌
    Signal To Noise Filtering For Peak Candidates 2 · holobiomicslab

    Use when immediately after peak detection in the IDSL.IPA workflow, when you have a list of candidate peaks extracted from EIC data and need to remove noise-dominated signals before downstream peak property evaluation and annotation.
    2 installs
58. ▌
    Mass Spectrometry Imaging Data Representation 2 · holobiomicslab

    Use when you have raw mass spectrometry imaging data (2D or 3D spatial coordinates with full mass-to-charge spectra) and want to train a probabilistic deep learning classifier for tumor delineation or tissue classification.
    2 installs
59. ▌
    Chromatography Mass Spectrometry Data Processing 2 · holobiomicslab

    Use when when you have raw GC–MS or LC–MS data (m/z vs retention time chromatography-mass spectrometry maps) and need to identify analyte signals and marker features without conventional peak picking;
    0 installs
60. ▌
    Metabolomics Software Benchmarking 2 · holobiomicslab

    Use when you have completed peak picking with two or more competing tools (e.g., IDSL.IPA, MZmine 2, xcms, MS-DIAL) on the same LC/HRMS dataset(s) and need to quantify which performs better. Use this skill when tool selection claims require validation (e.g., 'IDSL.
    0 installs
61. ▌
    Molecular Family Grouping Analysis 2 · holobiomicslab

    Use when you have untargeted metabolomics peak intensity data and spectral groupings (Molecular Families or Mass2Motifs) but lack confident chemical annotations or want to avoid pathway database dependency.
    0 installs
62. ▌
    Ms1 Feature Ranking And Extraction 2 · holobiomicslab

    Use when when you have raw LC-MS data files and need to identify which compounds were actually detected at high abundance during a gradient run, prior to evaluating whether the gradient provided good separation across the chemical space.
    0 installs
63. ▌
    Nmr Spectra Deep Learning Encoding 2 · holobiomicslab

    Use when when you have preprocessed 1H NMR spectral data from flavor mixtures or similar compound identification tasks, and you need to identify which compounds are present.
    1 install
64. ▌
    Noise Suppression Spectral Imaging 2 · holobiomicslab

    Use when your input is a raw two-dimensional MS map (m/z vs retention time) derived from chromatography–mass spectrometry data with poor signal-to-noise characteristics, and you need to discriminate individual analytes and identify marker features reliably.
    2 installs
65. ▌
    Nv Header Structure Interpretation 2 · holobiomicslab

    Use when you have a raw NV file from NMRViewJ or compatible NMR acquisition software and need to extract header metadata before processing spectroscopic data.
    0 installs
66. ▌
    Parameter Sharing Mechanism Design 2 · holobiomicslab

    Use when designing a contrastive learning pipeline for ion images or other data modalities where you need to process multiple augmented versions of the same input through an encoder and enforce similarity between the resulting representations.
    2 installs
67. ▌
    Pathway Ranking And Prioritization 2 · holobiomicslab

    Use when after peak annotation when you have: (1) a peak intensity matrix (rows=peaks with KEGG/ChEBI/UniProt IDs, columns=samples) with group labels; (2) a pathway database (KEGG, Reactome, or user-defined metabolite sets); (3) a comparative experimental design (case vs. control groups).
    2 installs
68. ▌
    Peak Picking Avoidance Ms Analysis 2 · holobiomicslab

    Use when analyzing raw 2D MS data (m/z vs. retention time maps) where conventional peak picking introduces unacceptable error rates, particularly in untargeted metabolomics or chemometrics studies requiring sensitive marker identification at trace levels (e.g., parts per billion).
    2 installs
69. ▌
    Peak Selectivity Metric Evaluation 2 · holobiomicslab

    Use when when identifying landmark peaks for retention time alignment in multi-sample LC-MS metabolomics workflows.
    0 installs
70. ▌
    Plant Metabolic Network Validation 2 · holobiomicslab

    Use when after community-dependent gap-filling has proposed reactions to fill metabolic gaps in individual consensus reconstructions.
    0 installs
71. ▌
    Regression Error Metric Evaluation 2 · holobiomicslab

    Use when when you have trained multiple regression models (e.g., using different feature sets: descriptors-only, fingerprints-only, or combined) on the same training data and need to objectively rank their generalization performance on unseen test data.
    0 installs
72. ▌
    Representation Collapse Prevention 2 · holobiomicslab

    Use when training a contrastive learning model on ion image data (mass spectrometry imaging) where augmented pairs of the same ion image must maximize similarity while different images minimize similarity.
    0 installs
73. ▌
    Retrieval Metric Hit K Calculation 2 · holobiomicslab

    Use when when you have generated embeddings for query and reference MS/MS spectra, computed a cosine similarity matrix between them, and need to evaluate how often the correct compound appears in the top-1, top-5, or top-10 retrieved candidates.
    0 installs
74. ▌
    Sample Capacity Constraint Setting 2 · holobiomicslab

    Use when when designing injection sequences for LC/GC-MS multi-omics experiments where you need to distribute samples across multiple plates and must account for mandatory QC sample positions (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, and custom QC).
    3 installs
75. ▌
    Spectral Adduct Ionmode Validation 2 · holobiomicslab

    Use when when processing raw or aggregated mass spectra datasets (from .mgf, .msp, .json, or .
    0 installs
76. ▌
    Spectral Library Msp Serialization 2 · holobiomicslab

    Use when after generating in-memory lipid spectra (with m/z, intensity, and metadata such as lipid class, fatty acid composition, and adduct type) when you need to export those spectra as a reusable MSP-format spectral library for downstream identification tasks in Excalibur, Skyline, or NIST MS.
    0 installs
77. ▌
    Spectral Data Preprocessing 2 · holobiomicslab

    Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct-injection MS (DI-MS), ASAP-MS, or other ambient ionization instruments (AI-MS, LDI-MS), and you need to identify peaks of interest, assign confidence scores, and prepare the data for database matching or species.
    0 installs
78. ▌
    Low Energy Structure Selection 2 · holobiomicslab

    Use when after generating an ensemble of 3D conformers via RDKit conformation sampling, when you need to reduce the conformer set size before expensive quantum-chemical calculations (e.g., QUICK).
    0 installs
79. ▌
    Quantum Input File Preparation 2 · holobiomicslab

    Use when you have a set of RDKit-generated conformers ranked by ASE-ANI single-point energies, and you need to submit the lowest-energy subset to quantum software (e.g. QUICK) for CCS-relevant electronic structure calculations.
    1 install
80. ▌
    Retention Time Range Filtering 2 · holobiomicslab

    Use when you have raw IM-MS data (Agilent MassHunter .d or UIMF format) and need to exclude early or late chromatographic regions—e.g., to skip dead volume, exclude blank runs, focus on a known analyte window, or reduce file size for faster processing.
    0 installs
81. ▌
    Smiles Adduct Form Enumeration 2 · holobiomicslab

    Use when when you have SMILES structures of small organic molecules and need to predict CCS values for metabolite annotation in untargeted mass spectrometry workflows. Specifically, apply this skill when the same chemical entity may appear in multiple ionization states (e.
    0 installs
82. ▌
    Structured Data Table Creation 2 · holobiomicslab

    Use when you have obtained a raw reference library file (such as the DTCCS_N2 library for U13C labeled lipids) and need to validate its structure, verify that all expected lipid entries are present, and ensure CCS values fall within physically plausible ranges (typically 50–300 Ų for small lipids).
    0 installs
83. ▌
    Chromatographic Data Structuring 2 · holobiomicslab

    Use when after parsing a centroid mzML file into (m/z, scan_number, intensity) tuples, when you need to organize sparse MS1 data for efficient peak detection and cross-sample alignment. Apply this skill when high mass resolution (e.
    0 installs
84. ▌
    Molecular Descriptor Computation 2 · 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
85. ▌
    Neural Network Module Validation 2 · holobiomicslab

    Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).
    2 installs
86. ▌
    Sample Replicate Pair Assessment 2 · 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
87. ▌
    Color Jitter Application Imaging 2 · 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
88. ▌
    M Z Window Tolerance Application 2 · 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.
    2 installs
89. ▌
    Marker Ion Ranking And Filtering 2 · 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
90. ▌
    Poisson Noise Injection Spectral 2 · 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
91. ▌
    Seurat Assay Metadata Extraction 2 · 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
92. ▌
    Substructure Annotation Integration 2 · holobiomicslab

    Use when you have created a GNPS molecular network (either classical or feature-based) and have computed MS2LDA motif assignments (probability and overlap scores) for the same spectra.
    0 installs
93. ▌
    Adduct Ion Prediction And Filtering 2 · holobiomicslab

    Use when when annotating m/z features against a metabolite database (HMDB, Lipidmaps, etc.) and the sample preparation, ionization method, or polarity mode favors specific adduct species. For example: negative-mode LC-MS or MS imaging will preferentially generate M-H and halide adducts (M+Cl);
    0 installs
94. ▌
    Adduct Ionmode Consistency Checking 2 · holobiomicslab

    Use when parsing, standardizing, or filtering MS spectra from mixed or heterogeneous databases where adduct assignment may be manually entered, auto-inferred, or missing.
    0 installs
95. ▌
    Biochemical Transformation Matching 2 · holobiomicslab

    Use when after you have detected and assigned molecular formulas to peaks in a single FT-ICR MS sample, and you want to infer which biochemical or abiotic reactions are occurring by examining pairwise mass differences.
    2 installs
96. ▌
    Collision Cross Section Computation 2 · holobiomicslab

    Use when you have a set of molecular structures in SMILES format that require CCS prediction for metabolite annotation in untargeted mass spectrometry workflows.
    2 installs
97. ▌
    Cross Domain Metadata Harmonization 2 · holobiomicslab

    Use when when you have submitted the same MS/MS spectrum query to multiple domain-specific MASST tools and need to compare matches, combine ranked results, or generate cross-domain summary statistics.
    2 installs
98. ▌
    Cross Reference Publication Linking 2 · 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
99. ▌
    Deep Learning Metabolite Annotation 2 · holobiomicslab

    Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible format) from a water sample, a precursor m/z and retention time of interest, and want to annotate an unknown compound by predicting its molecular formula, structure, and name using deep learning scoring rather than.
    2 installs
100. ▌
     Excel File Parsing For Metabolomics 2 · holobiomicslab

     Use when you have a preprocessed LC-MS peak table exported from peak-picking software (e.g., MS-DIAL) in Excel format with three logical compartments: sample annotation (rows), feature annotation (columns), and abundance matrix (numeric values).
     0 installs