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HolobiomicsLab

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1. ▌
   Peak Filtering And Quality Control · holobiomicslab

   Use when after peak picking and alignment have been performed on MSImagingArrays data (via peakPick() and peakProcess()), apply this skill when you need to remove noise-driven or low-frequency peaks before summarizing reference peaks across the full imaging dataset.
   2 installs
2. ▌
   Plant Nomenclature Standardization · holobiomicslab

   Use when when your metadata table contains species, genus, or family names that may be outdated, synonymous, or non-canonical, and you need to integrate them with the Literature Component (which requires standardized taxon identifiers) or cross-reference with external databases like Lotus Database.
   0 installs
3. ▌
   Pls Pls Da Classification Modeling · holobiomicslab

   Use when you have a preprocessed peak table (feature matrix with samples × peaks), known sample class labels or group membership, and a goal to classify or discriminate between two or more sample groups.
   0 installs
4. ▌
   Positional Encoding Implementation · holobiomicslab

   Use when you need to feed discrete chemical formula representations (e.g., 'C6H12O6') into a neural network that requires continuous vector inputs, particularly when adopting a transformer architecture for formula ranking or property prediction tasks.
   0 installs
5. ▌
   Precision Matrix Network Inference · holobiomicslab

   Use when you have a feature matrix (rows=samples, columns=features) and need to infer conditional independence structure among features, particularly when the true network is believed to be sparse and you want to control the sparsity level via regularization.
   0 installs
6. ▌
   Psm Rank Filtering Input Selection · holobiomicslab

   Use when you have a PSM file from a proteomics search engine containing multiple candidate identifications per spectrum and need to prepare input for rescoring with MS²Rescore. Use it when computational resources are limited or when you want to focus rescoring on high-confidence candidates (e.
   2 installs
7. ▌
   Psm To Spectrum Linking Validation · holobiomicslab

   Use when when you have PSM files from a proteomics search engine (e.g., MaxQuant, MSGFPlus, Mascot) and corresponding spectrum files (mzML or MGF format) that need to be linked before rescoring.
   0 installs
8. ▌
   Python Binary Io And Serialization · holobiomicslab

   Use when when you have mzPeak files (Parquet-based archives in uncompressed ZIP containers) or other PyArrow-compatible columnar formats containing mass spectrometry spectra, and you need to extract and decode spectral data arrays (m/z values, intensities) into Python memory for downstream.
   0 installs
9. ▌
   Qc Dilution Consistency Validation · holobiomicslab

   Use when after CV-based and blank-contribution filtering when you have untargeted metabolomics feature tables with QC samples that include dilution series (QC_half) and you need to ensure features exhibit consistent, approximately proportional intensity changes across dilution steps.
   0 installs
10. ▌
    Quantification Table Normalization · holobiomicslab

    Use when you have raw quantification data (abundance or intensity values across samples and features) from mass spectrometry or similar high-dimensional assays and need to prepare it for msFeaST's feature selection workflow, which requires standardized internal data structures compatible with.
    0 installs
11. ▌
    Quantile Normalization Application · holobiomicslab

    Use when after autoQ has extracted peak area measurements for isotopologues from GC-CI-MS data and you need to prepare these integrations for barplot visualization with metBarPlot.
    2 installs
12. ▌
    Queued Spectrum Preview Generation · holobiomicslab

    Use when when you have queued one or more spectral processing operations (e.g., smooth(), normalize(), reduceBaseline()) on an MSImagingArrays object and need to inspect the effect on representative spectra before processing the full dataset.
    1 install
13. ▌
    R Ggplot2 Multi Dimension Encoding · holobiomicslab

    Use when when you have tabular GO enrichment or gene set analysis results with at least 3–4 quantitative or categorical dimensions (e.
    0 installs
14. ▌
    R Internal Function Implementation · holobiomicslab

    Use when you need to expose capabilities of an external compiled dependency (e.g., a .NET assembly, C# wrapper, or executable) to R code, but direct R bindings do not exist.
    2 installs
15. ▌
    R Python Interoperability Bridging · holobiomicslab

    Use when when your analysis requires functionality from both R (statistical modeling, ROC analysis, caret machine learning) and Python (keras deep learning backend, numpy arrays) within a single R session, particularly for cross-language machine learning workflows like SERDA normalization that.
    0 installs
16. ▌
    R Script Configuration And Editing · holobiomicslab

    Use when you need to switch between Modular and Flow execution modes in LipidMatch/FluoroMatch, or when you need to change the analysis application type (PFAS analysis, Lipid analysis, or TWeen_pos analysis).
    2 installs
17. ▌
    R Script Execution And Integration · holobiomicslab

    Use when when you have pre-written R functions organized across multiple .R files (e.g., GSimp.R, GSimp_evaluation.R, Impute_wrapper.
    0 installs
18. ▌
    Recursive Algorithm Implementation · holobiomicslab

    Use when after peak detection on LC/HRMS data (mzXML, mzML, netCDF formats) when m/z values require refinement for improved mass accuracy in untargeted metabolomics workflows.
    0 installs
19. ▌
    Relative Log Abundance Calculation · holobiomicslab

    Use when after applying a normalization method (e.g., median scaling, RUV, RLSC) to metabolomics peak intensity data, when you need to visually assess whether normalization has successfully reduced batch effects and whether samples cluster appropriately by biological group.
    0 installs
20. ▌
    Repository Code Quality Assessment · holobiomicslab

    Use when you need to validate that all Python files in a repository meet the project's stated code formatting and style guidelines before merging a pull request, onboarding a new contributor, or establishing a baseline for code quality.
    2 installs
21. ▌
    Sample Group Injection Aggregation · holobiomicslab

    Use when when you have picked and annotated MS1 features from replicate injections of the same sample and need to produce a unified feature matrix indexed by sample (not injection).
    0 installs
22. ▌
    Saturation Threshold Configuration · holobiomicslab

    Use when when executing peak integration on preprocessed GC-IMS data (after alignment and baseline correction) and you need to decide whether to include or exclude peaks that exhibit saturation artifacts from the RIP signal. Set a threshold (e.g., 0.
    0 installs
23. ▌
    Seed Product Relationship Tracking · holobiomicslab

    Use when when applying biotransformation rules to seed metabolites to generate candidates, you need to record which rule produced each candidate and link it back to its parent seed structure. This is essential for downstream validation (e.
    0 installs
24. ▌
    Shiny App Configuration Deployment · holobiomicslab

    Use when you have built a Shiny application (global.R, ui.R, server.
    0 installs
25. ▌
    Side Chain Representation Learning · holobiomicslab

    Use when working with natural product molecules where conventional synthetic-molecule representations fail to capture synthesis patterns, and you need to encode both scaffold topology and the diverse chemical substituents (side chains) that distinguish natural product variants.
    0 installs
26. ▌
    Smiles Structure Format Validation · holobiomicslab

    Use when when you have raw molecular structures in SMILES or .sdf format and need to feed them into CypReact for CYP isoform prediction. Apply this skill before invoking the CypReact command-line tool to avoid runtime failures due to malformed input.
    0 installs
27. ▌
    Spatial Pixel Coordinate Alignment · holobiomicslab

    Use when you have mzML files from a mass spectrometry imaging (MSI) experiment and need to convert them to imzML format with correctly positioned pixel coordinates.
    0 installs
28. ▌
    Spatio Molecular Matrix Processing · holobiomicslab

    Use when you have deposited SpaceM spatio-molecular matrices (MORPHnMOL.
    0 installs
29. ▌
    Spectra Variable Metadata Handling · holobiomicslab

    Use when when designing a new MsBackend subclass or extending an existing backend to support mass spectrometry data import or representation.
    0 installs
30. ▌
    Spectral Search Result Aggregation · holobiomicslab

    Use when when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to consolidate results across domains (e.
    0 installs
31. ▌
    Storage Origin Metadata Assignment · holobiomicslab

    Use when when implementing or initializing an MsBackend subclass to handle mass spectrometry data, you must assign dataStorage and dataOrigin variables after loading m/z and intensity values.
    0 installs
32. ▌
    System Configuration Documentation · holobiomicslab

    Use when after successfully installing and validating all components of a complex multi-tool workflow (such as ENPKG), when you have confirmed that all dependencies resolve, external tools (e.g., Sirius, MZmine) are accessible at their expected paths, and test commands execute without error.
    0 installs
33. ▌
    T Test Interpretation Metabolomics · holobiomicslab

    Use when you have preprocessed, normalized, and imputed metabolite measurements organized in a MultiAssayExperiment object with two or more clearly defined sample groups (e.
    2 installs
34. ▌
    Table Record Filtering And Sorting · holobiomicslab

    Use when you have a table with multiple records (e.g., a protocol table with type, id, and description fields) and need to extract a subset of records matching a specific field criterion (e.
    0 installs
35. ▌
    Taxonomy Classification Evaluation · holobiomicslab

    Use when you have a pre-trained model (or candidate models) and need to assess whether it generalizes better than existing synthetic-molecule baselines on natural product taxonomy classification.
    0 installs
36. ▌
    Test Driven Development Validation · holobiomicslab

    Use when when you have implemented or modified a bioinformatic fingerprint generation function (or similar molecular computation module) and need to verify that: (1) the function accepts the correct input types (molecule objects from RDKit or equivalent), (2) it produces fixed-length numerical.
    0 installs
37. ▌
    Toml Configuration File Generation · holobiomicslab

    Use when when beginning a LipoCLEAN analysis workflow and needing to configure MS-DIAL export file locations, filtering parameters, and other tool options. Specifically when you have MS-DIAL 4 or MS-DIAL 5 exported data and need to prepare an options.txt file before running lipid quality filtering.
    0 installs
38. ▌
    Transfer Learning Model Adaptation · holobiomicslab

    Use when you have a pre-trained ABCoRT model checkpoint and a new chromatography dataset (e.g., Eawag_XBridgeC18_364.
    2 installs
39. ▌
    Unsaturation Degree Quantification · holobiomicslab

    Use when you have FT-ICR MS peak data with assigned molecular formulas (C, H, O, N, S, P elemental counts) and want to characterize the structural saturation and aromaticity of metabolites to assess their biochemical degradation potential, compare chemodiversity across samples, or stratify.
    0 installs
40. ▌
    User Override Parameter Management · holobiomicslab

    Use when punc'data's automatic keyword-based column recognition produces incorrect semantic role assignments—for example, when a column header contains a non-standard keyword that the tool fails to recognize, or when a column's true semantic role (e.
    2 installs
41. ▌
    Wine Windows Runtime Configuration · holobiomicslab

    Use when you have a Windows-only C# GUI application (e.g., AirdPro) built for .NET Framework 4.8 that needs to run on non-Windows hosts (macOS or Linux), and you are using a multi-stage Docker build where the runtime stage includes Wine and Windows compatibility libraries.
    0 installs
42. ▌
    Ms Imaging Spatial Metabolomics Workflow · holobiomicslab bundle

    Use when you have mass-spectrometry imaging data (imzML, e.g. MALDI/DESI) and want spatially-resolved metabolite annotations — pixel preprocessing and m/z alignment, FDR-controlled spatial annotation, spatial segmentation, and region-wise comparison.
    2 installs
43. ▌
    Bayesian Effect Size Moderation · holobiomicslab

    Use when after running DESeq2 differential expression analysis and extracting results with raw log fold changes, apply this skill when you observe high variance in effect size estimates across genes—particularly when many genes have small counts, unreliable variance estimates, or when you want.
    0 installs
44. ▌
    Gene Expression Linear Modeling · holobiomicslab

    Use when you have normalized or voom-transformed gene expression counts/intensities indexed by gene and sample, along with an experimental design matrix specifying condition, batch, or covariate assignments.
    0 installs
45. ▌
    K Mer Orientation Bug Diagnosis · holobiomicslab

    Use when a Rust port or alternative implementation of a mapper (e.g., salmon, piscem) consistently maps 2–3% more reads than a C++ reference, especially on short reads.
    2 installs
46. ▌
    Pathway Set Enrichment Analysis · holobiomicslab

    Use when you have normalized gene expression data (log-transformed, quantile-normalized) from a time-course or case-control experiment, a ranked gene statistic (e.g., mean expression, differential expression score), and a collection of curated gene sets (e.
    2 installs
47. ▌
    Rna Seq Count Matrix Generation · holobiomicslab

    Use when you have transcript-level abundance estimates from salmon, sailfish, or kallisto quantification and need gene-level count matrices for differential expression analysis.
    2 installs
48. ▌
    Rna Seq Count Normalization Tmm · holobiomicslab

    Use when apply TMM normalization when you have raw RNA-seq read counts from multiple samples and suspect differences in library composition (e.g., one sample over-represents a highly-expressed gene or transcript class relative to others).
    2 installs
49. ▌
    Bioconductor Data Import And Handling · holobiomicslab

    Use when you have CE-MS test files archived in the msdata Bioconductor package and need to load them into an in-memory or on-disk R representation to extract ion electropherograms, pick peaks, or compute effective mobility transformations.
    0 installs
50. ▌
    Mass Spectrum Fragment Ion Extraction · holobiomicslab

    Use when you have an experimental MS/MS spectrum (e.g., from MassBank or acquired data) for a single metabolite with known accurate precursor m/z and adduct type, and you need to generate a library entry with scored fragments for use in metabolite annotation pipelines.
    0 installs
51. ▌
    Normalization For Unequal Group Sizes · holobiomicslab

    Use when when tabulating chemical annotation enrichment (e.g., GNPS spectral library matches) across sample groups stratified by metadata category (e.g., sample type, extraction method, ionization source), and the groups contain different numbers of files or samples.
    0 installs
52. ▌
    Compound Data Subsetting By Threshold · holobiomicslab

    Use when you have a GC-MS dataset with a Match.Factor column (or equivalent quality metric) and need to evaluate how many unique compounds are retained at different confidence thresholds, or when you must subset the compound list to a user-defined quality level before downstream cheminformatics.
    2 installs
53. ▌
    Concentration Matrix Estimation Gc Ms · holobiomicslab

    Use when after GCMSFormer (or similar Transformer model) has predicted pure mass spectra (matrix S) for all components in overlapped GC-MS peaks, apply this skill to quantify the relative abundance of each component.
    0 installs
54. ▌
    Corpus Size Coverage Scaling Analysis · holobiomicslab

    Use when when deploying a Word2Vec-based spectral similarity model (such as Spec2Vec) on a new mass spectrometry dataset and needing to assess whether the pre-trained model's learned peak embeddings sufficiently represent the peaks in your query spectra.
    0 installs
55. ▌
    Cosine Similarity Spectral Clustering · holobiomicslab

    Use when you have a collection of deconvolved mass spectra (in MGF or mzTab format) from GC-MS analysis and need to group them into a molecular network to identify structural relationships and enable compound annotation.
    0 installs
56. ▌
    Gaussian Peakshape Fitting Evaluation · holobiomicslab

    Use when after peak detection on mass track segments using find_peaks, when you need to distinguish genuine chromatographic peaks from noise-induced false positives or irregular shapes.
    2 installs
57. ▌
    Mass Spectrometry Compound Extraction · holobiomicslab

    Use when you have a preprocessed GC-MS dataset (from spreadOut) with standardized column names (Compound.Name, Component.RT, Base.Peak.MZ, Component.Area, Match.Factor) and a specific list of chemical compounds you want to extract and aggregate across multiple sample runs.
    0 installs
58. ▌
    Mass Spectrometry Screening Workflows · holobiomicslab

    Use when when you have high-resolution LC-MS or GC-MS data from environmental samples and need to simultaneously screen for both known suspect chemicals and their transformation products, rather than targeting single compounds.
    1 install
59. ▌
    Metabolite Tandem Ms Library Curation · holobiomicslab

    Use when you have multiple tandem MS/MS libraries in different formats (msp, mgf) from different providers (NIST, RIKEN, MoNA, GNPS) with incomplete or inconsistent structural annotations (missing SMILES or molecular formula fields) and need to combine them into unified, polarity-specific msp files.
    0 installs
60. ▌
    Metabolomics Feature Table Conversion · holobiomicslab

    Use when you have generated a feature table via mzrtsim() with simulated LC/GC-MS abundances, condition assignments, and batch labels, and you need to pass it to Bioconductor tools (e.g., for batch correction, normalization, or statistical analysis) that expect SummarizedExperiment-class input.
    0 installs
61. ▌
    Module Dispatch Architecture Analysis · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (like mzmine) decides which processing module receives a given dataset based on its declared data type (LC vs. GC vs. IMS vs. MS imaging).
    0 installs
62. ▌
    Neutral Loss Extraction And Weighting · holobiomicslab

    Use when you have a collection of annotated MS/MS spectra with precursor m/z values and fragment peak lists, and you aim to train or apply a spectral similarity model (such as Spec2Vec Word2Vec) that exploits fragmentation chemistry.
    0 installs
63. ▌
    Noise Artifact Reduction Optimization · holobiomicslab

    Use when you have imported a raw GCxGC-MS chromatogram (NetCDF format folded into 2D-TIC) that exhibits chemical noise, instrumental artifacts, or baseline drift—conditions that obscure true metabolite signals and impede between-group differentiation in downstream multivariate analysis.
    0 installs
64. ▌
    Overlapped Peak Separation Evaluation · holobiomicslab

    Use when you have trained a GCMSFormer Transformer model on augmented simulated overlapped peaks and need to measure its generalization performance on unseen test data.
    0 installs
65. ▌
    Peak Feature Retention Time Alignment · holobiomicslab

    Use when you have preprocessed (smoothed and baseline-corrected) 2D-GCxGC-MS chromatograms from multiple samples and need to align their peak positions to a common reference chromatogram before multivariate analysis.
    0 installs
66. ▌
    Retention Time And Mass Based Sorting · holobiomicslab

    Use when you have raw GC-MS output in CSV format (with columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
    0 installs
67. ▌
    Retention Time Based Feature Grouping · holobiomicslab

    Use when after chromatographic peak detection on preprocessed LC-MS data when you have an xcms result object (XcmsExperiment or xcmsSet) with detected peaks and need to collapse redundant m/z signals into feature groups.
    0 installs
68. ▌
    Spectral Library Molecular Networking · holobiomicslab

    Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their similarity relationships, and identify spectral families without prior library matching.
    0 installs
69. ▌
    Spectral Similarity Scoring Ei Simple · holobiomicslab

    Use when you have a query electron ionization (EI) mass spectrum and need to search it against a library of known EI mass spectra to identify unknown compounds. Use it when exact identity matching (e.
    2 installs
70. ▌
    Temporal Profile Correlation Analysis · holobiomicslab

    Use when you have time-resolved direct injection mass spectrometry data (e.
    0 installs
71. ▌
    Two Dimensional Spectral Map Analysis · holobiomicslab

    Use when you have GC–MS or LC–MS data represented as a two-dimensional map with m/z values on one axis and retention time on the other, and you need to identify analyte signals and chemo-/biomarker features while minimizing false positive and false negative peak detections.
    3 installs
72. ▌
    Adduct Assignment Accuracy Assessment · holobiomicslab

    Use when you have a trained formula ranking model (such as MIST-CF) and want to measure the specific performance gain from incorporating multiple positive-mode adduct types (e.g., [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+) instead of restricting predictions to [M+H]+ only.
    0 installs
73. ▌
    Aird Format Conversion And Validation · holobiomicslab

    Use when you have vendor mass spectrometry raw files (e.g., .raw, .d, .
    0 installs
74. ▌
    Bandwidth Parameter Effect Comparison · holobiomicslab

    Use when you suspect XCMS grouping contains misaligned features due to suboptimal parameter settings or insufficient samples.
    2 installs
75. ▌
    Biological Reactant Pair Mapping Kegg · holobiomicslab

    Use when constructing or enriching a chemical formula database that must capture not just structural similarity (DBEdges) but also biological co-occurrence patterns.
    0 installs
76. ▌
    Chemical Fragmentation Event Tracking · holobiomicslab

    Use when when running a ViMMS Environment simulation with save_eval flag enabled and you need to correlate fragmentation events in the output mzML file back to their originating chemical compounds for downstream evaluation, optimization, or validation of acquisition strategies.
    0 installs
77. ▌
    Chromatographic Peak Characterization · holobiomicslab

    Use when after screening-mode validation of your m/z and retention time (RT) windows has confirmed that targets are visible in your data. Use it when you have centroided .mzML files, a validated target compound table with adjusted expected RT values (e.
    0 installs
78. ▌
    Chromatographic Peak Shape Comparison · holobiomicslab

    Use when after retention-time-based and abundance-correlation-based feature grouping have produced composite feature groups, and you need to identify which features within a group actually represent different compounds.
    0 installs
79. ▌
    Chromatographic Resolution Evaluation · holobiomicslab

    Use when when you have a feature table from LC-MS peak detection (e.g., output from MassCube's nontargeted peak segmentation step) and need to assess which features have adequate chromatographic separation from coeluting or nearby peaks.
    0 installs
80. ▌
    Compound Database Lookup And Curation · holobiomicslab

    Use when after feature extraction from LC–MS raw data (via XCMS, MS-Dial, or equivalent) has yielded a feature intensity table (samples × features) and feature metadata table (m/z, retention time, feature ID).
    0 installs
81. ▌
    Compound Standard Ratio Normalization · holobiomicslab

    Use when you have raw peak area or intensity measurements for both compounds and their corresponding internal standards across all study samples (including QC and calibration samples), and you need to normalize for instrument variability and injection efficiency before batch correction or quality.
    2 installs
82. ▌
    Compound Structure Comparison Metrics · holobiomicslab

    Use when you have two MS/MS spectra from related compounds (e.g., a reference compound and a suspected modified version) and need to quantify where and how their structures differ.
    2 installs
83. ▌
    Compound Structure Molecular Encoding · holobiomicslab

    Use when when you have SMILES strings or molecular structures for compounds and need to predict their retention behavior in reversed-phase liquid chromatography (RPLC) systems at pH ~2.7, but lack pre-computed molecular fingerprints or descriptor-based feature representations.
    1 install
84. ▌
    Configuration Driven Batch Processing · holobiomicslab

    Use when when processing multiple PSM files from search engines (e.g., MaxQuant, MSGFPlus, Mascot) that omit fixed modifications from their output, or when PSM and spectrum files use inconsistent ID schemes, decoy naming conventions, or modification notations.
    0 installs
85. ▌
    Cosine Similarity Scoring Computation · holobiomicslab

    Use when when you have imported and filtered mass spectrometry spectral data (from mzML, mzXML, msp, MGF, or JSON formats) and need to identify similar or related spectra within a dataset or against a reference library.
    2 installs
86. ▌
    Dda Fragmentation Strategy Simulation · holobiomicslab

    Use when you have real mzML LC-MS/MS data (e.g., from a Beer sample or HMDB reference set) and want to test whether a proposed TopN DDA strategy (or variant) can accurately reproduce the observed acquisition patterns, or you want to compare multiple acquisition controllers on the same chemical.
    0 installs
87. ▌
    Dda Mode Metabolomics Data Processing · holobiomicslab

    Use when when you have LC-MS/MS data collected in DDA mode and suspect that MS/MS spectra contain chimeric (multiply-charged or co-fragmented) ion signals that will degrade downstream spectral matching, library searching, or metabolite identification.
    0 installs
88. ▌
    Deep Learning Model Layer Composition · holobiomicslab

    Use when you have unpaired mass spectrometry spectra and need to predict Tanimoto-based molecular structural similarity scores between spectrum pairs.
    2 installs
89. ▌
    Dot Product Based Spectral Comparison · holobiomicslab

    Use when when searching an unknown MS/MS spectrum against a spectral library and you need to rapidly identify the most relevant candidate library spectra before applying cascade scoring with false discovery rate control.
    2 installs
90. ▌
    Extracted Ion Chromatogram Generation · holobiomicslab

    Use when you have raw MS data (in Agilent .d, Thermo .raw, Bruker .
    0 installs
91. ▌
    Extracted Ion Chromatogram Inspection · holobiomicslab

    Use when after running tardisPeaks() in screening mode or peak detection mode, when you need to visually confirm that target compounds are visible in the expected m/z and retention time windows, verify that peak integration boundaries are correct, diagnose whether sawtooth artefacts are present.
    0 installs
92. ▌
    Extracted Ion Chromatogram Processing · holobiomicslab

    Use when you have Thermo Fisher Orbitrap .raw files and need to locate and quantify specific peptide precursor ions (e.g., iRT calibrants, synthetic standards, or putative identifications).
    0 installs
93. ▌
    Feature Group Fragment Classification · holobiomicslab

    Use when you have a detected LC-MS feature table (with m/z, retention time, and intensity columns) and need to identify which features are derivatives of the same parent molecule rather than distinct metabolites.
    0 installs
94. ▌
    Feature Quality Assessment Via Qvalue · holobiomicslab

    Use when you have loaded search results from an upstream proteomics database search (e.g., OpenSwath, DIA-NN) containing feature identification data with Q-value scores, and you need to populate analyte dropdown menus or restrict downstream analysis to only statistically confident identifications.
    2 installs
95. ▌
    Fold Change Calculation Across Groups · holobiomicslab

    Use when when you have a quantified peak table (LC-MS feature intensities) with sample metadata assigning samples to discrete groups (e.
    0 installs
96. ▌
    Heavy Isotope Labeling Interpretation · holobiomicslab

    Use when your peptide sample has been enriched with stable isotope labels (13C, 15N, etc.) at a known incorporation probability (e.g., 52% 13C).
    2 installs
97. ▌
    Hotelling T Squared Outlier Detection · holobiomicslab

    Use when after data normalization (Step 7) on the preprocessed feature matrix when you need to identify and flag anomalous samples before statistical testing or biomarker discovery.
    0 installs
98. ▌
    Hyperdimensional Computing Projection · holobiomicslab

    Use when when clustering large-scale mass spectrometry datasets (millions of MS/MS spectra in MGF format) where runtime is a bottleneck and you have access to NVIDIA GPU resources (GTX 3090 for large datasets like PXD000561, or GTX 1080Ti for smaller datasets).
    0 installs
99. ▌
    Intensity Threshold Filtering Ms Data · holobiomicslab

    Use when when you have loaded aligned peak data (from a preceding molecular networking alignment task) as a structured table with peak intensity, m/z, retention time, and alignment quality metrics, and you need to reduce false positives, remove noise, or focus analysis on peaks above a.
    0 installs
100. ▌
     Ion Mobility Demultiplexing Algorithm · holobiomicslab

     Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired using multiplexed (compressed) ion mobility pulse sequences, and you need to recover conventional (non-multiplexed) IM-MS spectra with resolved mobility and mass dimensions.
     0 installs