← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

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

1. ▌
   Retention Time And Mass Sorting Of Chromatographic Peaks · holobiomicslab

   Use when you have raw GC-MS output from Agilent Unknowns Analysis (a .CSV with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
   0 installs
2. ▌
   Mass Spectrometry Domain Specific Language Comprehension · holobiomicslab

   Use when you need to translate user-facing mass spectrometry query intent (e.g., 'find all MS2 spectra with a precursor ion at m/z 572.
   0 installs
3. ▌
   Retention Time Projection Across Chromatographic Methods · holobiomicslab

   Use when when you have retention times measured on one chromatographic method and need to predict or map them to another method with minimal or no overlap in measured molecules.
   0 installs
4. ▌
   Tree Structure Optimization For Metabolite Deconvolution · holobiomicslab

   Use when you have a connected subnetwork of LC-MS features that matched isotope or adduct patterns, and you need to establish a canonical tree representation with a single neutral mass assignment.
   0 installs
5. ▌
   Editable Development Mode Installation And Verification · holobiomicslab

   Use when when you are developing or contributing to a Python package (like cooltools) and need to test changes to utility functions, library integrations, or API implementations without reinstalling the package after each modification. Apply this when you must verify that a new function (e.
   0 installs
6. ▌
   Python Collection Subclassing And Operator Overloading · holobiomicslab

   Use when you need to represent structured scientific data (e.g., molecular formulas with element–count mappings) as a dict-like object, but standard dict does not preserve type across arithmetic operations, does not support domain-specific validation, or lacks convenient string representations.
   0 installs
7. ▌
   Random Forest Classification For Metabolite Prediction · holobiomicslab

   Use when you have a metabolomics count table (rows=metabolites, columns=samples) with associated metadata containing a categorical grouping factor (e.
   0 installs
8. ▌
   Exact Mass Lookup And Aggregation From Chemical Databases · holobiomicslab

   Use when after loading raw Agilent Unknowns Analysis CSV output and when you need to convert tentative compound identifications (matched only by GC-MS library cosine similarity or Match.Factor score) into searchable, curated chemical records with exact masses and multi-source confirmation.
   0 installs
9. ▌
   Mass Spectrometry Compound Annotation Database Generation · holobiomicslab

   Use when after generating transformation products using generateTPs() with structural information (SMILES), when you need to screen for predicted TP compounds in environmental MS/MS data via MetFrag's in-silico fragmentation annotation.
   0 installs
10. ▌
    Search Result Integration With Raw Mass Spectrometry Data · holobiomicslab

    Use when when you have completed a DIA-MS proteomics search (e.
    1 install
11. ▌
    Transcription Factor Motif Genomic Coordinate Annotation · holobiomicslab

    Use when you have ATAC-seq BAM files and want to detect transcription factor footprints—characteristic depletion patterns of Tn5 insertions around protein-bound motif sites.
    0 installs
12. ▌
    Multi Regime Model Performance Comparison Visualization · holobiomicslab

    Use when you have paired microbiome-metabolome (or similar multivariate) datasets and want to quantify whether training on a superset of features (e.g., both annotated and unannotated metabolites) improves prediction accuracy for a well-defined target subset (e.
    0 installs
13. ▌
    Benchmark Dataset Generation From Reference Metabolites · holobiomicslab

    Use when you have a set of centroided mzML files from LC-HRMS analysis, a list of target metabolites with known molecular formula and retention time windows, and you need to create a reference dataset to benchmark the reliability of NPP tools (XCMS, MZmine, MS-DIAL, etc.) on the same files.
    0 installs
14. ▌
    Chemical Transformation Prediction Via Rule Application · holobiomicslab

    Use when you have: (1) a set of starting compounds in SMILES format; (2) a library of reaction rules (SMARTS-encoded) from MetaCyc or custom sources; (3) a need to discover predicted reaction products and novel compounds across multiple reaction generations; and (4) constraints (e.
    0 installs
15. ▌
    Compression And Serialization Of Large Tabular Datasets · holobiomicslab

    Use when when consolidating multiple cleaned and validated data sources (organism, structure, reference subgraphs) into a single denormalized table containing hundreds of thousands of rows and many columns, and the result must be stored, archived, or transmitted with minimal storage overhead while.
    2 installs
16. ▌
    Dictionary And Metadata Extraction From Relational Data · holobiomicslab

    Use when after performing left-join operations on cleaned organism, structure, and reference subgraphs but before final table denormalization. Trigger conditions: (1) you have a unified table with repeated entity_id columns (e.
    0 installs
17. ▌
    Environment Variable Configuration For Distributed Jobs · holobiomicslab

    Use when you have a multi-fold cross-validation training workflow that must run as parallel SLURM array jobs, each with its own GPU, and you need to ensure that all jobs can locate the same training data, code repository, container image, and results directory without hardcoded absolute paths or.
    0 installs
18. ▌
    Heterogeneous Data Format Integration And Harmonization · holobiomicslab

    Use when your input consists of multiple external databases with different file formats, column names, identifier schemes, and taxonomic/chemical vocabularies (e.g., 31 open natural product databases with heterogeneous structure and organism metadata).
    0 installs
19. ▌
    Metabolite Compound List Mapping With Adduct Assignment · holobiomicslab

    Use when when you have mzML files from targeted or untargeted metabolomics experiments run in multiple ionization modes (e.g., KO_NEG, KO_POS, STD_NEG, STD_POS, WT_NEG, WT_POS) and a CSV list of reference compounds (e.
    0 installs
20. ▌
    Open Source Mass Spectrometry File Format Interoperability · holobiomicslab

    Use when when working with Bruker .d/.baf mass spectrometry imaging data and needing to feed it into MSIGen or other open-source MSI processing pipelines.
    0 installs
21. ▌
    Image Processing On Two Dimensional Mass Spectrometry Maps · holobiomicslab

    Use when when you have raw GC–MS data in two-dimensional m/z × retention time format (NetCDF or proprietary binary) and need to identify marker features across aroma or breath samples at parts-per-billion concentration levels, particularly when conventional peak picking introduces false positives.
    0 installs
22. ▌
    Computational Efficiency Single Pass Vs Repeated Detection · holobiomicslab

    Use when when processing aligned LC-MS data across multiple samples where the computational bottleneck is repeated peak-detection algorithm calls (one per sample per m/z value). Typical scenario: >10 samples with >1000 m/z values each, where N individual find_peaks invocations dominate runtime.
    0 installs
23. ▌
    Kernel Regression Learning From Spectral Fingerprint Pairs · holobiomicslab

    Use when when you have a training set of MS2 spectra with known chemical structures (e.
    1 install
24. ▌
    Mass Spectrometry Feature Extraction From Cardinal Objects · holobiomicslab

    Use when you have a Cardinal MSImagingExperiment object (e.g., from imzML or Analyze 7.5 files) and need to retrieve the complete set of m/z values and their intensities for annotation against metabolite databases (HMDB, Lipidmaps) or for statistical analysis.
    0 installs
25. ▌
    Mass Spectrum Tokenization And Bag Of Fragments Generation · holobiomicslab

    Use when after filtering and cleaning MS/MS spectra (positive/negative ion mode) but before applying Latent Dirichlet Allocation for Mass2Motif discovery.
    0 installs
26. ▌
    Metabolite Cluster Identification From Correlated Features · holobiomicslab

    Use when after preprocessing, imputation, and batch correction of LC-MS peak tables when you need to group redundant or related feature measurements (e.g., [M+H]+ and [M+Na]+ adducts, or isotope peaks) into metabolite-level clusters before statistical testing or identification.
    0 installs
27. ▌
    Software Performance Characterization And Scaling Analysis · holobiomicslab

    Use when when a tool claims to be 'scalable' or 'performance-conscious' but lacks published performance benchmarks, or when you need to confirm that runtime and memory scale linearly (or predictably) with sample count before deploying the tool on large LC-MS datasets (e.g., >100 samples).
    0 installs
28. ▌
    Chemical Name Normalization And Publish Database Integration · holobiomicslab

    Use when after spreadOut() has converted raw CSV peak data into a structured list, when you have one or more Compound.Name entries from GC-MS that may be ambiguous, non-canonical, or missing standardized properties (exact mass, published retention times, reactive groups, database presence).
    0 installs
29. ▌
    Backend Compatibility Verification Visualization Library · holobiomicslab

    Use when you have mass spectrometry data loaded into a pandas DataFrame with m/z, retention time, and intensity columns, and need to confirm that pyOpenMS-Viz can produce visualizations (spectra, chromatograms, or peak maps) using a specific plotting backend (matplotlib, Bokeh, or Plotly) on real.
    0 installs
30. ▌
    Command Line Pipeline Execution And Runtime Benchmarking · holobiomicslab

    Use when when you have peak-abundance .csv files and assigned molecular formula data from FT-ICR MS preprocessing, and you need to verify that a published pipeline's runtime claims (e.g., '<1 min for 40 samples', '~2 min for 120 samples') hold true on your own datasets or reference datasets.
    0 installs
31. ▌
    Data Transformation Centered Log Ratio With Pseudocounts · holobiomicslab

    Use when you have raw microbiome (e.g., 16S rRNA or metagenomic) or metabolomic count tables (samples × features) and plan to train predictive models (e.g., MiMeNet, linear regression) that require normally distributed or near-normally distributed inputs.
    2 installs
32. ▌
    Feature Attribution Score Interpretation Neural Networks · holobiomicslab

    Use when after training a neural network model (e.
    0 installs
33. ▌
    Chemical Identifier Mapping Smiles To Pubchem Chemspider · holobiomicslab

    Use when you have a chemical structure in SMILES format and need to find matching compound records and standardized identifiers (e.
    0 installs
34. ▌
    Fingerprint Computation Maccs Extended Connectivity Path · holobiomicslab

    Use when when you have a set of chemical compounds (as SMILES, mol, SDF, mol2, or hin files) and need to convert their structural information into numerical fingerprint vectors for training machine learning regressors on experimental retention time data or other molecular property prediction tasks.
    0 installs
35. ▌
    Natural Product Database Querying Norine Coconut Npatsas · holobiomicslab

    Use when you have a chemical structure (as SMILES string or identifier) and need to discover matching records across specialized natural product databases.
    0 installs
36. ▌
    Principal Component Analysis Dimensionality Reduction · holobiomicslab

    Use when your input is a normalized, centered gene expression matrix with many genes (e.g., 12,000+) and you need to validate whether reducing to a smaller number of principal components (e.g., 10) preserves pathway enrichment statistics (pathway scores and p-values from geseca or fgsea).
    1 install
37. ▌
    Pytest Test Suite Execution And Result Interpretation · holobiomicslab

    Use when after forking and cloning a repository (e.g., scverse/scanpy) to verify that the development environment is correctly configured, or after implementing a feature or bugfix to ensure no regressions were introduced.
    0 installs
38. ▌
    Single Cell Rna Seq Quality Control And Normalization · holobiomicslab

    Use when when you have a raw or minimally processed scRNA-seq dataset (e.g., a Seurat object loaded from GEO) and need to prepare it for pathway enrichment or coregulation analysis.
    0 installs
39. ▌
    Microbiome Metabolome Data Preprocessing Clr Transformation · holobiomicslab

    Use when you have paired microbiome and metabolomic abundance tables (samples × features) with relative abundance or raw count values, and you are preparing data for downstream regression or neural network modeling of microbe-metabolite relationships.
    2 installs
40. ▌
    Tandem Mass Spectrometry Ion Fragmentation Pattern Analysis · holobiomicslab

    Use when after MS1 feature extraction and prescreening quality control have completed on mzML files, and you need to inspect the MS2 fragmentation patterns of candidate compounds to verify their identity or assess whether extracted features are genuine metabolites rather than noise or artifacts.
    2 installs
41. ▌
    Model Generalization Assessment Across Molecular Size Regime · holobiomicslab

    Use when a deep learning model for molecular structure prediction (e.g., NMR2Struct) has been trained and evaluated on a limited molecular size range (e.
    0 installs
42. ▌
    Distance Metric Calculation Bray Curtis Euclidean Jaccard · holobiomicslab

    Use when you have normalized peak intensity data (or absence/presence matrices) from metabolomics experiments with multiple samples and need to quantify compositional differences between them prior to multivariate analysis. This step is essential when testing whether categorical factors (e.
    0 installs
43. ▌
    Microbe Metabolite Feature Selection By Annotation Status · holobiomicslab

    Use when when you have paired microbiome-metabolome datasets where only a subset of metabolites carry curated biochemical annotations (e.
    0 installs
44. ▌
    Spatial Correlation Analysis In Imaging Mass Spectrometry · holobiomicslab

    Use when after annotating ion pairs with known adducts (using adductMatch or diffGetPeaks), use this skill to filter suspected adduct pairs by testing if their pixel-level intensity profiles are significantly correlated.
    0 installs
45. ▌
    Functional Annotation Table Generation And Interpretation · holobiomicslab

    Use when after running CPAT, signalP, Pfam, and fimo tools on differentially expressed isoform or exon FASTA sequences, and you need to consolidate their individual outputs into a single indexed table to compare functional properties across isoforms, identify isoforms with specific domain.
    0 installs
46. ▌
    Machine Learning Model Evaluation With Confusion Matrices · holobiomicslab

    Use when after fitting a random forest model to metabolomics count data with a categorical response variable (e.g., wild-type vs. knockout treatment groups), you need to quantify how accurately the model predicts group membership and identify which metabolites drive the classification.
    0 installs
47. ▌
    Metabolomicshub Cross Repository Dataset Search · holobiomicslab

    Use when assembling a reanalysis or meta-analysis cohort from public metabolomics studies held in MetaboLights, Metabolomics Workbench and GNPS/MassIVE, and the instrument, polarity or open-format filters have to be honest about which repositories they silently exclude.
    0 installs
48. ▌
    Chromatographic Peak Extraction And Retention Time Filtering · holobiomicslab

    Use when when you have LC-MS/MS raw data (mzML or netCDF format) and need to isolate a specific compound's signal based on its known or suspected m/z value and retention time range.
    0 installs
49. ▌
    Baseline And Noise Level Estimation From Quartile Statistics · holobiomicslab

    Use when before peak detection on a composite or individual mass track when you need to filter out low-intensity noise and baseline drift without removing true signal.
    0 installs
50. ▌
    Cheminformatics Substructure Matching And Reaction Templates · holobiomicslab

    Use when you have a chemical substrate and need to predict its biotransformation products using rule-based metabolism prediction. This applies when: (1) you possess a library of biotransformation rules extracted from a curated database (e.
    0 installs
51. ▌
    Interactive Mass Spectrometry Plot Generation And Annotation · holobiomicslab

    Use when when you have extracted ion chromatograms (XICs), ion mobilograms (IMs), or mass spectra from diaPASEF or other DIA workflows and need to visualize them interactively to inspect peak boundaries, compare MS1 vs MS2 traces, validate feature identifications, or communicate results.
    2 installs
52. ▌
    Ion Chromatogram Mobilogram Visualization And Interpretation · holobiomicslab

    Use when after loading raw diaPASEF or DIA mass spectrometry data (mzML format) and search results (DIA-NN, OpenSwath, or equivalent) to visually inspect extracted ion chromatograms and mobilograms for selected peptide precursors.
    0 installs
53. ▌
    Training Data Inventory Construction From Spectral Libraries · holobiomicslab

    Use when you are preparing to apply Probability Product Kernel–based scoring to MS2 spectra for genomic–metabolomic linking, and you need to establish a reference set of ion peaks that represent robust spectral diversity without overfitting to any single study.
    0 installs
54. ▌
    Sphinx Documentation Generation And API Reference Inclusion · holobiomicslab

    Use when after implementing or modifying utility functions in a library subpackage (e.g., cooltools.
    0 installs
55. ▌
    Metabolite Class Visualization By Statistical Significance · holobiomicslab

    Use when after running omu_summary statistical comparison on count data with assigned hierarchical class annotations (KEGG, KO_Number, Prokaryote, or Eukaryote), use this skill to visualize log2FoldChange and adjusted p-values for metabolites grouped by class.
    0 installs
56. ▌
    Tensor Shape Validation And Numerical Correctness Checking · holobiomicslab

    Use when after implementing a shared-weight ResNet18 encoder module but before integrating it into the DeepION data augmentation and projection workflow.
    1 install
57. ▌
    Alternative Splicing Event Comparison Across Conditions · holobiomicslab

    Use when you have PSI (percent-spliced-in) matrices calculated independently for two or more biological conditions, each with two or more replicate samples, and you want to identify which alternative splicing events show statistically significant changes in inclusion levels between conditions.
    0 installs
58. ▌
    Metabolite Detection And Acquisition Performance Benchmarkin · holobiomicslab

    Use when you have simulated or experimental mzML data from two or more fragmentation controllers (e.
    2 installs
59. ▌
    Interactive Visualization Interpretation Methylation Results · holobiomicslab

    Use when after running ChAMP detection functions (champ.
    0 installs
60. ▌
    Deep Learning Model Implementation In Pytorch Or Tensorflow · holobiomicslab

    Use when when you need to construct a dual-branch neural network encoder that processes two augmented versions of the same input (e.g., ion images in COL or ISO mode) and must enforce weight sharing between branches to reduce parameters while maintaining separate output representations.
    0 installs
61. ▌
    Feature Count Verification Across Adducts And Isotopologues · holobiomicslab

    Use when after mzRAPP has exported a benchmark CSV file from centroided mzML files and you need to confirm the benchmark was constructed correctly before using it to evaluate NPP tool performance. Specifically, when you have a reference expectation (e.
    0 installs
62. ▌
    Natural Products Structure Organism Association Integration · holobiomicslab

    Use when you have separately cleaned and validated tables for organisms (interim/tables/2_cleaned/organism/cleaned.tsv.gz), structures (interim/tables/1_translated/structure/final.tsv.gz and interim/tables/2_cleaned/structure/named.tsv.gz), references (interim/tables/2_cleaned/reference/cleaned.tsv.
    0 installs
63. ▌
    Posterior Parameter Estimation For Metabolite Distributions · holobiomicslab

    Use when you have metabolomics data with left-censored missing values (below detection limit) and need to impute them.
    0 installs
64. ▌
    Resnet Architecture Modification For Dimensionality Control · holobiomicslab

    Use when your task requires a pretrained convolutional encoder (ResNet18) to produce fixed-size representation vectors of a specific dimensionality (e.g., 512 dimensions) rather than the default output size.
    0 installs
65. ▌
    Signal Preprocessing Chain Normalization Smoothing Baseline · holobiomicslab

    Use when apply this preprocessing chain when you have loaded raw or continuous imzML mass spectra into a Cardinal MSImagingArrays object and need to prepare them for peak picking, statistical analysis, or imaging.
    1 install
66. ▌
    Boundary Case Read Classification Via Sequence Alignment · holobiomicslab

    Use when when two mapping implementations (or versions of the same mapper) show disagreement on per-read mapping status—e.g., one mapper leaves reads fully unmapped that the other maps, or one maps with high confidence where the other is uncertain.
    0 installs
67. ▌
    Two Dimensional Correlation Optimized Warping Parameter Tuni · holobiomicslab

    Use when when you have a preprocessed sample chromatogram (smoothed and baseline-corrected) and a preprocessed reference chromatogram, and need to align them using 2D COW.
    0 installs
68. ▌
    Positional Distribution Profile Aggregation And Visualizatio · holobiomicslab

    Use when you have ATAC-seq BAM alignments with classified motif sites (bound vs. unbound based on chromatin accessibility or binding thresholds) and wish to detect and visualize the characteristic Tn5 insertion depletion signal (footprints) around transcription factor binding sites.
    0 installs
69. ▌
    Correlation Analysis Between Experimental Computational Data · holobiomicslab

    Use when you have paired experimental and computational predictions for the same biological property (e.
    0 installs
70. ▌
    Microbial Phage Infection Experimental Design Interpretation · holobiomicslab

    Use when you have a bacterium-phage infection study with normalized peak intensities from FT-ICR MS across multiple phage treatment groups (minimum 2–3 conditions such as HP1, HS2, control) and sample replicates (n ≥ 6–8 per group), and you need to test whether phage-type factor explains.
    0 installs
71. ▌
    Metabolite Biomarker Classification Via Unsupervised Project · holobiomicslab

    Use when after preprocessing GCxGC-MS chromatograms (smoothing, baseline correction, peak alignment) when you need to uncover latent metabolite patterns that distinguish biological groups without prior class labels. Specifically useful for exploratory separation of disease states (e.
    2 installs
72. ▌
    Metabolomic Spectral Annotation And Molecular Family Cluster · holobiomicslab

    Use when when you have raw or GNPS-processed MS2 spectral data from microbial strains and need to organize spectra into molecular families (grouped by spectral similarity) while preserving strain provenance, as a prerequisite for linking metabolomic families to gene cluster families (GCFs) via.
    0 installs
73. ▌
    Molecular Structure Ground Truth Matching And Accuracy Evalu · holobiomicslab

    Use when after an end-to-end neural model (CNN + transformer) has generated predicted molecular structures (formula and connectivity) from 1D NMR spectra.
    1 install
74. ▌
    Random Access And Sequential Iteration Pattern Implementatio · holobiomicslab

    Use when when you need to support fast, non-sequential lookups (e.
    0 installs
75. ▌
    Spearman Correlation Coefficient Calculation Cross Validatio · holobiomicslab

    Use when you have trained predictive models (e.g., MiMeNet neural networks) on microbiome-metabolome paired data using k-fold cross-validation, held out test folds for each fold-iteration, and generated continuous abundance predictions for metabolites.
    0 installs
76. ▌
    Computational Performance Benchmarking And Timing Measuremen · holobiomicslab

    Use when when you need to validate that a newly published bioinformatics pipeline meets stated performance claims, or when you must characterize how execution time scales with dataset size (sample count, peak count, or formula complexity) and optional analysis features (e.
    0 installs
77. ▌
    Mass Spectrometry Adduct Nomenclature And Formula Transforma · holobiomicslab

    Use when you have a neutral molecular formula (e.g., C3H8O2) and need to compute the adducted formula that will actually be observed in MS data;
    0 installs
78. ▌
    Metabolite Chemodiversity Index Calculation And Interpretati · holobiomicslab

    Use when you have peak-abundance data (after molecular formula assignment, peak filtering by m/z, isotope, ppm error, and sample presence thresholds) and you need to quantify and compare the molecular composition diversity across samples or conditions.
    2 installs
79. ▌
    Galaxy Workflow4metabolomics Reproducible Processing · holobiomicslab

    Use when running an LC-MS or GC-MS preprocessing and statistics pipeline on a Galaxy Workflow4Metabolomics instance, or when a collaborator must re-execute the analysis without installing the toolchain — the stage order is fixed by the wrappers' own datatypes, not by convention.
    0 installs
80. ▌
    Extraction Parameter Optimization Ppm Retention Time Ion Mob · holobiomicslab

    Use when you are reconstructing targeted ion chromatograms (XIC) and ion mobilograms (IM) from raw diaPASEF data and need to balance sensitivity (wide extraction windows) against specificity (narrow windows that reject interference).
    0 installs
81. ▌
    Differential Chromatin Accessibility Analysis Between Cell T · holobiomicslab

    Use when you have pre-processed chromatin accessibility data (ATAC-seq or DNAse-seq) with chromVAR deviations already computed for individual cells or bulk samples across multiple cell types or conditions, and you need to identify which transcription factor motifs exhibit significant differential.
    0 installs
82. ▌
    Score Distribution Analysis And Statistical Significance Tes · holobiomicslab

    Use when after computing a scoring function over all possible genomic-metabolomic candidate pairs (e.g., all 2966 MIBiG-GNPS BGC-spectrum pairs), when you have a subset of known validated links and need to assess whether the scoring function ranks them significantly higher than expected by chance.
    0 installs
83. ▌
    Thermodynamic Molecular Index Calculation From Elemental Com · holobiomicslab

    Use when when you have peak-abundance .csv files with assigned molecular formulas (elemental composition: C, H, O, N, P, S) from FT-ICR MS or high-resolution MS and need to characterize the redox and structural properties of the molecular pool—e.
    0 installs
84. ▌
    Molecular Formula To Carbon Count Extraction · holobiomicslab

    Use when when you have a feature list from HRMS data with molecular formula annotations (inferred or assigned) and need to compute per-carbon mass defect ratios (MD/C, m/C) as part of PFAS candidate prioritization.
    0 installs
85. ▌
    Molecular Networking Parameter Configuration · holobiomicslab

    Use when after preparing a feature table and MS/MS spectral data (mzML or MGF format with precursor m/z, retention time, and MS/MS spectra) and before submitting to GNPS for molecular network generation.
    0 installs
86. ▌
    Multi Component Weighted Ranking Aggregation · holobiomicslab

    Use when you have completed LC–MS/MS feature detection and annotation (via MZmine2/3 and GNPS/SIRIUS/CANOPUS), have compiled a taxonomically annotated metadata table, and need to rank extracts by their likelihood of containing novel chemistry.
    2 installs
87. ▌
    Multiple Linear Regression Model Application · holobiomicslab

    Use when when you have an observed m/z value from mass spectrometry imaging and need to annotate it with a ranked list of candidate chemical formulae. Apply this skill when the KnownSet database (2.
    0 installs
88. ▌
    Mzml Format Output Generation And Validation · holobiomicslab

    Use when after running a ViMMS simulation loop with a fragmentation controller (e.
    0 installs
89. ▌
    Neutral Loss Feature Extraction From Spectra · holobiomicslab

    Use when you have MS2 spectra data (MGF/mzML format) and aligned feature tables, and your analysis goal is to compare samples that may have poor MS1 feature overlap, strong retention-time shifts across runs, or were acquired on different LC-MS platforms.
    0 installs
90. ▌
    Non Targeted Feature Detection And Screening · holobiomicslab

    Use when you have raw LC/MS data in mzML format and your analysis goal is to comprehensively detect and annotate all mass spectral features present, rather than measuring predefined target analytes.
    0 installs
91. ▌
    Orbitrap Spectrum Acquisition Interpretation · holobiomicslab

    Use when when you have a Thermo Scientific .raw file from an Orbitrap instrument (e.
    0 installs
92. ▌
    Pairwise Similarity Scoring Weighted Metrics · holobiomicslab

    Use when after anchor selection and RT mapping spline fitting, when you have a fitted metabCombiner object with pre-aligned feature pair candidates and need to determine which parameter weights (A for RT, B for m/z, C for similarity score) discriminate true metabolite matches from false positives.
    0 installs
93. ▌
    Peak Detection And Alignment In Metabolomics · holobiomicslab

    Use when after generating simulated mzML output from ViMMS and you need to compare it against real acquisition data. Specifically, use it when you have paired real and simulated mzML files from the same sample (e.g., Beer1pos) and must evaluate whether a fragmentation strategy (e.
    0 installs
94. ▌
    Peak Quality Metric Interpretation Alignment · holobiomicslab

    Use when when you have loaded aligned peak-alignment data from a molecular networking task and need to distinguish high-confidence, reproducible peak alignments from noise or spurious matches.
    0 installs
95. ▌
    Performance Threshold Filtering And Analysis · holobiomicslab

    Use when when a trained model produces probabilistic or ensemble predictions and you need to achieve a specific target accuracy metric (e.g., RMSE ≤ 0.1) or minimize error on a test set, but the unfiltered model does not meet that target.
    0 installs
96. ▌
    Pipeline End To End Execution And Validation · holobiomicslab

    Use when you have a published computational pipeline with deposited code and validation data, and you need to verify that the pipeline can be executed end-to-end to reproduce reported validation metrics (annotation accuracy, coverage, or equivalent performance benchmarks).
    2 installs
97. ▌
    Principal Coordinate Analysis Interpretation · holobiomicslab

    Use when when you have computed pairwise distances between MS2 fingerprint vectors from multiple metabolomics samples and need to visualize sample similarity relationships in low dimensions.
    0 installs
98. ▌
    Reaction Filtering By Substrate Completeness · holobiomicslab

    Use when you have loaded intracellular metabolomics data (LC-MS normalized abundances) and a stoichiometric metabolic model with multiple reactions, and you plan to compute reaction propensity scores or other flux-related metrics that depend on substrate concentrations.
    0 installs
99. ▌
    Retention Time Alignment Mapping Application · holobiomicslab

    Use when after mass tracks have been aligned across samples into a MassGrid structure and retention time calibration dictionaries (rt_cal_dict) have been computed for each sample, but before summing intensity vectors element-wise to construct the composite map.
    0 installs
100. ▌
     Retention Time Calibration Lowess Regression · holobiomicslab

     Use when after mass track construction and before composite map building, when you need to align retention times across multiple LC-MS samples. Trigger conditions: (1) you have identified high-selectivity landmark peaks (mSelectivity > 0.99) in a reference sample;
     0 installs