← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

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

1. ▌
   Coordinate System Normalization 1based Indexing · holobiomicslab

   Use when when exporting quantified ion images and pixel metadata from LipidQMap to HDF5 format for use in downstream Cardinal or other MSI analysis workflows.
   0 installs
2. ▌
   Core Spectra Variable Definition And Population · holobiomicslab

   Use when when implementing a custom MsBackend class for the Spectra package, you must define these two methods to satisfy the MsBackend virtual class API contract.
   0 installs
3. ▌
   Elution Profile Normalization And Preprocessing · holobiomicslab

   Use when when you have raw co-fractionation/mass-spectrometry elution intensity profiles and plan to train a CNN or semi-supervised learning model (Label Spreading) directly on unengineered elution data.
   0 installs
4. ▌
   Extracted Ion Chromatogram Parameter Extraction · holobiomicslab

   Use when after isolating TIC peak regions via sliding window analysis and peak expansion (isolatePeaks), apply this skill when you need dataset-specific XCMS parameter estimates.
   0 installs
5. ▌
   Hierarchical Clustering Dendrogram Construction · holobiomicslab

   Use when when you have a Metaboprep object after quality control filtering and need to visualize metabolite correlation structure to: (1) identify clusters of co-regulated features that may represent the same biological pathway or measurement artifact, (2) set tree-cutting height thresholds for.
   0 installs
6. ▌
   High Dimensional Similarity Search Optimization · holobiomicslab

   Use when when you have a large spectral library (thousands to millions of spectra) represented as high-dimensional vectors and need to match unknown query spectra against it, but exhaustive pairwise comparison is computationally prohibitive.
   0 installs
7. ▌
   Internal Standard Ion Selection And Application · holobiomicslab

   Use when after isotope correction has been applied to MSI ion images, when you have sprayed or identified a reference lipid standard of known amount (pmol/mm²) and need to normalize target lipid intensities against this standard to remove matrix effects and enable cross-pixel and cross-sample.
   0 installs
8. ▌
   Lchrms Chromatographic Peak Boundary Extraction · holobiomicslab

   Use when you have a set of target molecules with known molecular formula, main adduct, and experimentally determined retention time boundaries, and you want to extract their chromatographic peaks and isotopologues from LC-HRMS mzML files to generate a ground-truth benchmark for validating.
   2 installs
9. ▌
   Machine Learning Model Selection And Comparison · holobiomicslab

   Use when when you have a preprocessed metabolomics feature matrix with labeled samples and need to determine which classifier (traditional ML vs. deep learning) predicts the phenotype of interest.
   0 installs
10. ▌
    Mass Offset Scanning For Modification Detection · holobiomicslab

    Use when you have a query mass spectrum of unknown modification status and need to search a spectral library to identify the peptide and its post-translational modifications.
    0 installs
11. ▌
    Mass Spectrometry Imaging Vendor Format Support · holobiomicslab

    Use when your input mass spectrometry imaging data is in a proprietary vendor format (Bruker .d/.baf, or other binary formats not natively supported by MSIGen) and you need to convert it to an open, readable format (mzML or processed binary) compatible with MSIGen's msigen() function.
    0 installs
12. ▌
    Mass Spectrometry Peak Detection And Extraction · holobiomicslab

    Use when you have raw high-resolution mass-spectrometry data in mzML or mzXML format from breath analysis and need to identify individual volatile organic compounds before sample-to-sample alignment or comparative analysis.
    0 installs
13. ▌
    Metabolite Feature Visualization Across Batches · holobiomicslab

    Use when after applying batch-effect correction methods (parametric ComBat, non-parametric ComBat, ber, or ber-bagging) to log-transformed metabolomics abundance matrices, use this skill when you need to visually inspect whether technical heterogeneity (drift across batch, signal shift) has been.
    0 installs
14. ▌
    Metabolite Prediction Cyp450 Enzyme Specificity · holobiomicslab

    Use when you have a small-molecule query (acetaminophen, drug candidate, xenobiotic, or other compound as SMILES or SDF) and need to predict which metabolites would be formed if that molecule were metabolized by a defined subset of the nine major human CYP450 isoforms (1A2, 2A6, 2B6, 2C8, 2C9.
    2 installs
15. ▌
    Metabolomic Data Normalization Post Integration · holobiomicslab

    Use when immediately after integrating multiple metabolomic datasets from different analytical experiments into a unified feature-by-sample matrix. Batch effects manifest as systematic unwanted variations correlated with analytical batch rather than biological sample groups;
    0 installs
16. ▌
    Metabolomics Analyte Stability Characterization · holobiomicslab

    Use when you are designing a blood sampling protocol for metabolomics or lipidomics analysis and need to predict whether specific analytes (polar metabolites or lipids) will degrade under planned pre-analytical conditions (e.
    2 installs
17. ▌
    Metabolomics Data Exclusion Criteria Validation · holobiomicslab

    Use when you have received or published a claim about the number of metabolites excluded by a missingness-based quality filter (e.g., 'cutoff=0.
    2 installs
18. ▌
    Multi Tool Result Integration And Harmonization · holobiomicslab

    Use when when you have completed parallel or sequential tool runs (e.g., CPAT, signalP, Pfam, fimo) on the same set of sequences and need to create a unified functional annotation table, summary statistics, or cross-tool comparison report.
    0 installs
19. ▌
    Network Topology Analysis For Bgc Deduplication · holobiomicslab

    Use when when you have a collection of tokenised BGCs (each gene represented as Pfam domain tokens) and need to remove near-duplicate or highly similar clusters before detecting biosynthetic sub-clusters.
    0 installs
20. ▌
    Python Bracket Notation Protocol Implementation · holobiomicslab

    Use when you have a blockwise-indexed compressed file (e.g., indexed gzip with chapter or spectrum identifiers) and need to retrieve individual logical blocks by key using Python bracket notation (e.g., `handler['chapter_1']` or `handler[0]`) rather than sequential iteration.
    0 installs
21. ▌
    Python Class Implementation With Dunder Methods · holobiomicslab

    Use when you have mzML spectral data stored in a non-standard format (SQLite database, custom binary store, or indexed archive) and need pymzML's Reader to parse and iterate over spectra as if they were in native mzML files. Specifically, when FileInterface.
    0 installs
22. ▌
    Sciex Multiquant Data Export Format Recognition · holobiomicslab

    Use when you have txt files exported from Sciex MultiQuant (>v3.0.3) containing QCpool samples measured at regular intervals during mass spectrometry sequences, and you need to validate whether the file structure is compatible with the QComics package before parsing and quality assessment.
    2 installs
23. ▌
    Smarts Pattern Design For Microbial Degradation · holobiomicslab

    Use when you need to predict small molecule metabolism in soil or aquatic microbiota and must translate published biotransformation rules (reaction types, enzyme families, substrate patterns) from EAWAG or similar biodegradation databases into executable chemical pattern-matching rules compatible.
    0 installs
24. ▌
    Spatial Transcriptome Metabolome Coregistration · holobiomicslab

    Use when you have paired spatial transcriptome and metabolome datasets (both as h5ad files with .obsm['spatial'] coordinate matrices and .
    0 installs
25. ▌
    Spectral Data Compression By Frame And Mobility · holobiomicslab

    Use when you have raw IM-MS data in Agilent MassHunter (.d) or UIMF format from drift tube (DT) or SLIM instruments, and you need to reduce data volume while preserving signal integrity for subsequent HRdm demultiplexing and peak deconvolution.
    1 install
26. ▌
    Structure Similarity Search Across Repositories · holobiomicslab

    Use when you have a SMILES string or chemical structure and need to determine whether it exists in public chemical repositories, or locate reference identifiers and metadata for the same compound across multiple authoritative sources.
    0 installs
27. ▌
    Transcript Abundance Quantification With Salmon · holobiomicslab

    Use when you have adapter-trimmed FASTQ files and need to obtain transcript-level abundance estimates without performing full genomic alignment.
    2 installs
28. ▌
    Unit Test Design For Cheminformatics Algorithms · holobiomicslab

    Use when you have implemented a custom Filter subclass (e.g., Tanimoto sampling, metabolomics matching, or target filtering) in minedatabase/filters.py and need to verify that similarity scoring, scaling transformations (e.
    0 installs
29. ▌
    Univariate Statistical Testing For Metabolomics · holobiomicslab

    Use when you have paired metabolomics count data (metabolite abundance matrix) and sample metadata with categorical treatment or experimental factor assignments, and you need to test for statistically significant differences in individual metabolite abundances between exactly two groups (t-test) or.
    1 install
30. ▌
    Euclidean Distance Computation Approximation · holobiomicslab

    Use when when constructing k-nearest neighbor graphs from spatial coordinates (e.g., microscopy x,y positions or tissue section coordinates) and exact neighbor discovery is computationally prohibitive;
    0 installs
31. ▌
    Pearson Correlation Computation Across Tools · holobiomicslab

    Use when you have quantification results from two or more independent implementations, versions, or variants of the same analysis tool (e.g. C++ salmon 1.11.
    0 installs
32. ▌
    Spatial Neighbor Graph Properties Validation · holobiomicslab

    Use when after calling squidpy.gr.spatial_neighbors on an AnnData object containing spatial coordinates in obsm.
    2 installs
33. ▌
    Spectral Coverage And Intensity Metric Computation · holobiomicslab

    Use when you have completed a ViMMS simulation run or processed real LC-MS/MS data and need to quantitatively assess whether one DDA controller (e.g., WeightedDEWController with exclusion) outperforms another (e.g., TopNController) in terms of spectral coverage and signal recovery.
    2 installs
34. ▌
    Spectral Similarity Scoring And Reference Matching · holobiomicslab

    Use when when you have extracted MS2 spectra from DDA chromatographic peaks and need to identify the originating compound by comparing against reference MS2 spectra (e.g., from Metlin or GNPS).
    0 installs
35. ▌
    Exact Mass Utilization For Compound Identification · holobiomicslab

    Use when you have a GC-MS dataset in CSV format with retention times, base peak m/z values, component areas, and compound names, and you need to identify whether specific query chemicals are present in your samples and retrieve their -match factors (scoring the confidence of the spectral match) and.
    0 installs
36. ▌
    Biosynthetic Gene Cluster Mining With Genomic Data · holobiomicslab

    Use when you have LC-MS/MS spectra (MGF, mzXML, mzML, or mzData format) from a bacterial or fungal strain and corresponding genomic sequence data (FASTA, antiSMASH .final.gbk, or BOA .annotated.
    0 installs
37. ▌
    Cascade Search Strategy For Peptide Identification · holobiomicslab

    Use when use this strategy when analyzing tandem mass spectrometry data where you expect both unmodified and modified peptide identifications and require high confidence assignments with controlled false discovery rates.
    2 installs
38. ▌
    Expressionset Construction And Metadata Annotation · holobiomicslab

    Use when after validating a peak table (either standardized format or software tool–generated format) and its corresponding label file, before applying any NOREVA assessment functions (normulticlassqcall, nortimecourseqcall, etc.).
    2 installs
39. ▌
    Feature Matrix Preparation For Supervised Learning · holobiomicslab

    Use when you have preprocessed metabolomics feature abundance data and want to train multiple classifiers (traditional ML or deep learning) to predict sample phenotype or disease status.
    0 installs
40. ▌
    Mass Spectrometry Workflow Orchestration Snakemake · holobiomicslab

    Use when when you have a collection of mzML.gz files from a multidimensional MS instrument (e.
    2 installs
41. ▌
    Metabolite Annotation Integration Across Databases · holobiomicslab

    Use when you have MZmine-aligned features with m/z and retention time, and you have generated spectral annotations from two or more database sources (e.g., GNPS/ISDB spectral matching and SIRIUS in silico structure elucidation).
    0 installs
42. ▌
    Metabolomic Feature Statistical Hypothesis Testing · holobiomicslab

    Use when when you have a normalized and batch-corrected feature abundance matrix from non-targeted LC-MS/MS metabolomics (e.
    0 installs
43. ▌
    Metabolomics Chemical Mixture Generation From Hmdb · holobiomicslab

    Use when you need to create realistic, diverse chemical populations for simulating LC-MS/MS acquisition strategies in a virtual environment. It is essential when you lack real metabolomics data but want to prototype and compare fragmentation strategies (e.
    2 installs
44. ▌
    Molecular Fingerprint Extraction And Vectorization · holobiomicslab

    Use when you have annotated metabolite structures (with SMILES strings) from a reference library (e.
    0 installs
45. ▌
    Molecular Structure Reconstruction From Embeddings · holobiomicslab

    Use when you have a pretrained encoder that produces fixed-size embeddings from MS/MS spectra (or other molecular data modalities) and you need to recover the corresponding molecular structure as a SMILES string.
    0 installs
46. ▌
    Neutral Loss Extraction From Fragmentation Spectra · holobiomicslab

    Use when preparing MS/MS spectra for bag-of-fragments conversion and LDA-based motif discovery. You have raw spectra in supported formats (.mgf, .mzML, or .
    0 installs
47. ▌
    Parameter Range Filtering For Chromatographic Data · holobiomicslab

    Use when you have raw MS data in instrument-native or mzML format (Agilent .d, Thermo .raw, Bruker .d) and need to isolate specific analyte regions defined by precise m/z windows, RT windows (in seconds or minutes), and/or ion mobility arrival-time windows.
    0 installs
48. ▌
    Peak Boundary Identification In Extracted Ion Data · holobiomicslab

    Use when after extracting ion chromatograms and ion mobilograms from raw diaPASEF or DIA data within specified m/z, retention time, and ion mobility windows.
    0 installs
49. ▌
    Spectral Embedding Extraction From Neural Networks · holobiomicslab

    Use when you have a set of preprocessed MS/MS spectra (binned to 10,000 m/z bins with intensities square-root transformed) and a trained MS2DeepScore Siamese neural network model, and you need to compute 200-dimensional spectral embeddings for dimensionality reduction, clustering, or chemical space.
    0 installs
50. ▌
    Structural Clustering Validation In Chemical Space · holobiomicslab

    Use when you have trained or loaded a deep learning model that produces high-dimensional spectral embeddings (e.g., 200-dimensional vectors from MS2DeepScore base network) and need to validate that these embeddings capture chemical structure information rather than learning spurious patterns.
    0 installs
51. ▌
    Unknown Pollutant Identification Mass Spectrometry · holobiomicslab

    Use when you have UPLC-HRMS raw data (ThermoFisher, Agilent, or compatible vendor format) from water samples or environmental matrices containing unknown organic pollutants, a Windows environment with ≥16 GB RAM and ≥2 GB NVIDIA GPU, and you need compound identification with confidence scores and.
    0 installs
52. ▌
    Metabolite Phenotype Association Partial Correlation · holobiomicslab

    Use when you have a SummarizedExperiment object containing NMR or MS metabolomic data with aligned phenotype information (BMI, disease status, age, gender), and you need to identify metabolites associated with a continuous or categorical outcome while controlling for known confounders that might.
    0 installs
53. ▌
    Nmr Inadequate Spectra Acquisition And Preprocessing · holobiomicslab

    Use when when you have raw INADEQUATE NMR spectral data (e.g., from a query sample or library) and need to extract peak coordinates and intensities as a first step toward identifying metabolite peak networks or comparing against a metabolite database.
    0 installs
54. ▌
    Pytest Unit Test Execution And Coverage Reporting · holobiomicslab

    Use when after implementing or modifying Python library functions (such as utility functions in cooltools.lib subpackages) to verify correctness and identify gaps in test coverage before merging changes or releasing code.
    3 installs
55. ▌
    Spectral Embedding Dimension Reduction Parameters · holobiomicslab

    Use when after generating a tile matrix or feature count matrix from single-cell ATAC-seq, RNA-seq, Hi-C, or methylation data, before clustering or UMAP visualization, when you need unsupervised dimension reduction that scales to millions of cells and is agnostic to the underlying data modality.
    2 installs
56. ▌
    Artifact Size Measurement And Range Verification · holobiomicslab

    Use when you have built multiple Docker image variants (e.g., cli, dev, linux, windows) from a multi-stage Dockerfile and need to verify that their uncompressed and compressed storage footprints fall within documented acceptable ranges (e.
    0 installs
57. ▌
    Confidence Score Extraction From Neural Networks · holobiomicslab

    Use when when you have a trained deep learning model (e.g., PS2MS) and an evaluation dataset of compounds, and you need to assess how prediction confidence varies across structural novelty classes (e.g., training-similar vs. structurally novel NPS analogues).
    2 installs
58. ▌
    Github Actions Workflow Inspection And Execution · holobiomicslab

    Use when a GitHub repository displays a CI workflow badge (e.g., passing/failing status in README) and you need to verify that the reported status is accurate, reproduce the CI environment locally, or debug workflow failures.
    0 installs
59. ▌
    Graph Neural Network Architecture Implementation · holobiomicslab

    Use when you have a baseline GNN model trained on a molecular property prediction task (e.
    2 installs
60. ▌
    Message Passing Variant Selection And Adaptation · holobiomicslab

    Use when you have a baseline GNN model for predicting a continuous molecular property (e.
    0 installs
61. ▌
    Molecular Dataset Partitioning And Preprocessing · holobiomicslab

    Use when you have raw molecular datasets (e.g., METLIN-CCS, CCSBase) with SMILES strings, 3D coordinates, adduct information, and ground-truth collision cross section labels, and you need to format them for GNN training and held-out test evaluation with consistent standardization.
    0 installs
62. ▌
    Reference Dataset Validation For Metabolite Ions · holobiomicslab

    Use when after computing expected adduct ions for a metabolite using a derivatizing matrix ruleset, validate the predicted m/z values and adduct formulas against a curated reference dataset that documents which ions are actually produced by that matrix under standard ionization conditions.
    1 install
63. ▌
    Statistical Distribution Analysis Across Cohorts · holobiomicslab

    Use when when you have prediction scores (softmax probabilities, uncertainties) from a trained deep learning model evaluated on a heterogeneous dataset and you need to determine whether prediction confidence or accuracy varies systematically across structurally distinct or novel compound.
    0 installs
64. ▌
    Command Line Tool Installation And Configuration · holobiomicslab

    Use when before launching any MetaboDirect pipeline run on a new system or environment. Trigger conditions: (1) first-time setup on a target OS (Windows, Linux, or macOS); (2) environment lacks Python 3.5+, R 4.0+, or Cytoscape 3.8+;
    0 installs
65. ▌
    Compound Class Assignment From Molecular Formula · holobiomicslab

    Use when after peaks have been filtered (by m/z, isotopic presence, and formula assignment error) and you have a list of peaks with assigned molecular formulas.
    0 installs
66. ▌
    Concentration Prediction From Calibration Curves · holobiomicslab

    Use when when you have a targeted metabolomics peak area intensity table with samples classified into calibration curve standards (with known concentration values), quality control (QC) samples, blanks, and unknowns, and you need to convert raw peak intensities into predicted concentrations for.
    2 installs
67. ▌
    Dimension Scale Linking And Cross Group Indexing · holobiomicslab

    Use when when exporting quantified MSI data as HDF5 containers following the Cardinal::HDF5 layout convention, and you need to establish bidirectional indexing between intensity data (feature-by-pixel matrix) and metadata groups (featureData, pixelData).
    0 installs
68. ▌
    Dimensionality Reduction For Batch Visualization · holobiomicslab

    Use when after data preprocessing and standardization of a metabolomics feature matrix, when you need to detect and visually characterize batch effects arising from known experimental conditions, unknown latent groups, or hidden substructures before formal statistical testing.
    2 installs
69. ▌
    Feature Intensity Preservation Across Correction · holobiomicslab

    Use when when you have loaded a raw MS quantification table (feature-by-sample intensity matrix) into QuantyFey and are applying drift-correction strategies (Internal Standard correction, statistical drift correction, Custom Bracketing, or Weighted Bracketing) but need to maintain traceability.
    1 install
70. ▌
    Feature Table Annotation And Provenance Tracking · holobiomicslab

    Use when after generating a filtered feature table from raw mass spectrometry data in openNAU.
    0 installs
71. ▌
    Metabolite Prediction Comparison Baseline Models · holobiomicslab

    Use when you have paired microbiome (genus-level 16S or functional profiles) and metabolome datasets (e.g., mass spectrometry or metabolomics panels) with 100+ samples, and you want to demonstrate that a new prediction method outperforms prior work.
    0 installs
72. ▌
    Metabolomics Normalization Artifact Reproduction · holobiomicslab

    Use when you have raw metabolomics intensity data (rows = compounds, columns = samples) with batch annotations and QC/biological sample labels, and you need to select among five normalization methods.
    2 installs
73. ▌
    Multidimensional Feature Detection And Alignment · holobiomicslab

    Use when when you have acquired LC-IMS-MS/MS data (mzML or mzML.gz format) from multiple samples and need to detect features that exploit simultaneous separation in m/z, drift time, and retention time to improve detection sensitivity and reduce false positives.
    0 installs
74. ▌
    Peak Apex Identification From Intensity Profiles · holobiomicslab

    Use when after EIC candidate generation and peak detection have been completed on LC/HRMS data, when you need to extract the retention time and intensity values at peak maxima for each detected peak.
    0 installs
75. ▌
    Reference Peak Matching Retention Time Alignment · holobiomicslab

    Use when you have training LC-HRMS chromatograms (rt × m/z matrix format) from which you have already extracted peak candidates using smoothing and gradient-descent peak detection, and you possess a curated reference list of isolated single chromatographic peaks (ground truth).
    0 installs
76. ▌
    Regex Pattern Design For Value Format Validation · holobiomicslab

    Use when when you have a metabolomics metadata table and need to automatically identify and standardize database-ID columns (HMDB_ID, PubChem_ID, KEGG_ID, etc.) whose values follow known format conventions.
    2 installs
77. ▌
    Repository Match Consolidation And Deduplication · holobiomicslab

    Use when use this skill after parallel or sequential dispatch queries to multiple chemical repositories have returned results. Specifically: (1) you have received match records from two or more of {PubChem, ChemSpider, Norine, ChEBI, COCONUT, NP Atlas} with differing schemas or identifiers;
    0 installs
78. ▌
    Reproducibility Statistic Computation Rank Based · holobiomicslab

    Use when you have high-dimensional replicate experiment data (metabolomics, proteomics, or genomics) with multiple biological or technical replicates per sample, and you need to assess which features are reproducible across replicates and which sample pairs show consistent reproducibility patterns.
    0 installs
79. ▌
    Sample Pair Filtering By Feature Reproducibility · holobiomicslab

    Use when when you have a Marr() output object containing reproducibility statistics from replicate experiments, and your goal is to retain only those sample pairs (i,i') where reproducibility is robust across the majority of features.
    2 installs
80. ▌
    Single Cell Spatial Metabolomics Data Processing · holobiomicslab

    Use when you have raw IMC and SIMS image data from the same tissue region(s) and need to: (1) register the two modalities spatially, (2) segment individual cells across both images, (3) extract per-cell protein and metabolite intensity vectors, and (4) prepare the data for downstream joint analysis.
    0 installs
81. ▌
    Smiles Tokenization And Canonical Representation · holobiomicslab

    Use when when preparing SMILES strings as training targets for a sequence-to-sequence decoder that reconstructs molecular structures from embeddings.
    0 installs
82. ▌
    Species Authentication Classification Evaluation · holobiomicslab

    Use when when you have high-throughput mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other ambient ionization formats) from unknown biological samples and need to determine their species identity against a curated reference database.
    0 installs
83. ▌
    Spectral Library Matching With Cosine Similarity · holobiomicslab

    Use when you have a query spectrum and a reduced candidate set of library spectra (via approximate nearest neighbor indexing), and need to search for exact unmodified peptide matches with high confidence before proceeding to variable-mass-shift modification searches.
    0 installs
84. ▌
    Missing Value Imputation For Omics · holobiomicslab

    Use when your metabolomic peak table contains missing values (e.g., undetected metabolites below instrument sensitivity or sparse measurements) and you are preparing multi-class or time-course data for statistical analysis, differential profiling, or biomarker discovery.
    0 installs
85. ▌
    Mixed Effects Model Interpretation · holobiomicslab

    Use when your metabolomics dataset contains hierarchical or repeated structure (e.g., multiple samples per batch, multiple compounds per internal standard group, or QC replicates measured across runs) and you need to model the relationship between a continuous outcome (e.
    2 installs
86. ▌
    Model Metadata Endpoint Validation · holobiomicslab

    Use when after starting a TensorFlow Serving instance (e.g., via docker-compose) and before attempting classification tasks, to confirm that input layers are named 'input_2048' and 'input_4096' and the output layer is named 'output'.
    1 install
87. ▌
    Model Serving Artifact Preparation · holobiomicslab

    Use when you have trained Keras models that need to be deployed in a TensorFlow Serving container, and the serving infrastructure requires HDF5 TensorFlow 2.0+ format with specific input/output layer naming conventions (e.g., 'input_2048', 'input_4096', 'output').
    0 installs
88. ▌
    Module Eigenmetabolite Calculation · holobiomicslab

    Use when after metabolic correlation modules have been identified via hierarchical clustering with dynamic branch cutting on a biweight midcorrelation matrix. Apply this skill when you need a single representative abundance profile per module to correlate against sample traits (e.
    0 installs
89. ▌
    Molecular Structure Transformation · holobiomicslab

    Use when when you have native metabolite structures (SMILES or mol format) and need to predict adduct ions for a mass spectrometry imaging experiment that uses a derivatizing matrix known to produce ions other than common [M+H]+ (positive mode) or [M-H]- (negative mode).
    0 installs
90. ▌
    Msi Intensity Matrix Normalization · holobiomicslab

    Use when after isotope correction when you have extracted intensity matrices from imzML or HDF5 MSI data and need to convert raw or isotope-corrected ion-image intensities into quantified values using a known internal standard lipid species.
    2 installs
91. ▌
    Msimagingarray Object Manipulation · holobiomicslab

    Use when when you have loaded mass spectrometry imaging data into a MSImagingArrays object in Cardinal 3.6 and need to explore the effects of multiple preprocessing steps (e.
    0 installs
92. ▌
    Msms Spectrum Object Instantiation · holobiomicslab

    Use when when you have successfully resolved a USI string to extract raw spectrum data from an online proteomics/metabolomics repository (PRIDE, MassIVE, etc.) and need to construct a spectrum object that exposes spectrum data as Python attributes and methods for downstream processing (filtering.
    2 installs
93. ▌
    Msp File Parsing And Serialization · holobiomicslab

    Use when you have raw .msp files containing mass spectra records and need to extract spectrum identifiers (compound name, precursor mass, retention time) as structured data for enrichment via external web services, or you have enriched spectrum objects and must write them back to .
    0 installs
94. ▌
    Multi Source Metabolite Resolution · holobiomicslab

    Use when you have metabolite identifiers sourced from a single metabolome database (e.
    0 installs
95. ▌
    Multi Task Learning Feature Fusion · holobiomicslab

    Use when when you have multi-branch deep learning architecture predicting related but distinct peptide properties (charge state, isotope count, retention time) from raw mass spectrum, and you want to leverage auxiliary task gradients to improve primary task learning.
    0 installs
96. ▌
    Natural Product Structure Encoding · holobiomicslab

    Use when you have natural product molecules in SMILES, InChI, or SDF format and need to convert them into fixed-length numerical feature vectors for downstream machine learning tasks (e.g., biosynthetic class prediction, molecular similarity analysis, or chemical space exploration).
    1 install
97. ▌
    Network Layout Algorithm Selection · holobiomicslab

    Use when you have a network object (nodes and edges) loaded in MetaNet and need to compute 2D or 3D spatial coordinates for visualization. This skill is necessary before any network plotting step. Choose this when your network structure (e.
    0 installs
98. ▌
    P Value Cutoff Threshold Filtering · holobiomicslab

    Use when after differential expression analysis (DEA) has produced p-values and log fold-change values for multiple omics layers (genes, miRNA, proteins, lipids), and you need to select only statistically significant features for pathway enrichment.
    2 installs
99. ▌
    Pathway Kernel Association Testing · holobiomicslab

    Use when you have paired genotype and phenotype data and want to test for association between a predefined genetic pathway (set of genes or variants) and a quantitative or binary trait, particularly when individual-variant tests lack power or when pathway-level aggregation is scientifically.
    0 installs
100. ▌
     Peak Detection Accuracy Assessment · holobiomicslab

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