← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 7.4k skills
• 0 followers
• 2 days ago last updated

1. ▌
   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
2. ▌
   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
3. ▌
   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
4. ▌
   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
5. ▌
   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
6. ▌
   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
7. ▌
   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
8. ▌
   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
9. ▌
   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
10. ▌
    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.
    0 installs
11. ▌
    Temporal Profile Correlation Analysis · holobiomicslab

    Use when you have time-resolved direct injection mass spectrometry data (e.
    0 installs
12. ▌
    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.
    0 installs
13. ▌
    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
14. ▌
    Aird Format Conversion And Validation · holobiomicslab

    Use when you have vendor mass spectrometry raw files (e.g., .raw, .d, .
    0 installs
15. ▌
    Bandwidth Parameter Effect Comparison · holobiomicslab

    Use when you suspect XCMS grouping contains misaligned features due to suboptimal parameter settings or insufficient samples.
    0 installs
16. ▌
    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
17. ▌
    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
18. ▌
    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
19. ▌
    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
20. ▌
    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
21. ▌
    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
22. ▌
    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.
    0 installs
23. ▌
    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.
    0 installs
24. ▌
    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.
    0 installs
25. ▌
    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
26. ▌
    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.
    0 installs
27. ▌
    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
28. ▌
    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
29. ▌
    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.
    0 installs
30. ▌
    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.
    0 installs
31. ▌
    Extracted Ion Chromatogram Generation · holobiomicslab

    Use when you have raw MS data (in Agilent .d, Thermo .raw, Bruker .
    0 installs
32. ▌
    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
33. ▌
    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
34. ▌
    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
35. ▌
    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.
    0 installs
36. ▌
    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
37. ▌
    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).
    0 installs
38. ▌
    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
39. ▌
    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
40. ▌
    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
41. ▌
    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
42. ▌
    Ion Type Classification And Filtering · holobiomicslab

    Use when you have an MS/MS spectrum and a ProForma 2.0 peptidoform specification, and you need to identify which observed peaks correspond to specific fragment ion types (e.g., only b and y ions for backbone fragmentation, or immonium ions for amino acid identification).
    0 installs
43. ▌
    Isotope Pattern And Adduct Assignment · holobiomicslab

    Use when after feature detection has produced a TSV feature table (from Asari or equivalent) containing m/z, retention time, and intensity columns, and before MS1 or MS2 annotation.
    0 installs
44. ▌
    Isotopic Pattern Mispicking Detection · holobiomicslab

    Use when you have a peak table from tandem MS preprocessing (e.g., MS-DIAL, Metaboscape) and suspect that isotopic patterns have been incorrectly split during feature detection.
    0 installs
45. ▌
    Landmark Peak Selection And Filtering · holobiomicslab

    Use when when preparing mass tracks for retention-time (RT) alignment across multiple LC-MS samples.
    0 installs
46. ▌
    Lc Ms Feature Alignment Cross Dataset · holobiomicslab

    Use when you have two peak-picked, conventionally aligned LC-MS metabolomics datasets (e.
    0 installs
47. ▌
    Lipid Retention Time Rule Application · holobiomicslab

    Use when you have candidate lipid annotations from spectral library matching (e.g., XCMS + CAMERA output) with MS/MS scores, and you need to reduce false positives and predict previously unannotated lipids.
    0 installs
48. ▌
    Mass Charge Retention Time Validation · holobiomicslab

    Use when after loading centroided .mzML LC-MS data and creating a target list with compound ID, name, theoretical or measured m/z, expected RT (in minutes), and polarity designation, perform this validation step to confirm target visibility and refine m/z and RT window parameters before running.
    0 installs
49. ▌
    Mass Error Calculation And Validation · holobiomicslab

    Use when when annotating observed mass spectrometry peaks against theoretical fragment ions (b, y, or other ion types) using ProForma 2.0 peptidoforms, compute the m/z deviation for each matched peak to verify that the annotation adheres to your specified mass tolerance (e.g., ±10 ppm or ±0.
    0 installs
50. ▌
    Mass Range Filtering For Metabolomics · holobiomicslab

    Use when when preparing a chemical database for virtual or real MS/MS acquisition, and you need to focus on a specific m/z window (e.g., 100–1000) that matches your instrument's scan range or your metabolomics study's analytical scope.
    0 installs
51. ▌
    Mass Spectrometry Data Format Parsing · holobiomicslab

    Use when you have raw MS/MS spectra in one of the supported exchange formats (.mgf, .mzML, or .msp) and need to ingest them into an MS2LDA pipeline for unsupervised motif discovery. This skill is required before any preprocessing, filtering, or ionization-mode-specific handling can occur.
    0 installs
52. ▌
    Mass Spectrometry Data Interpretation · holobiomicslab

    Use when you have a set of ions already matched to a khipu instance (i.e., ions whose isotope and adduct assignments are known and positioned on the theoretical khipu grid), and you need to estimate the neutral mass of the parent compound.
    0 installs
53. ▌
    Mass Spectrometry Data Representation · holobiomicslab

    Use when you need to store or retrieve mass spectrometry spectra (m/z and intensity pairs) from a novel data source or storage medium (e.
    0 installs
54. ▌
    Mass Spectrometry File Format Parsing · holobiomicslab

    Use when you have raw MS/MS spectral data in one or more standard mass spectrometry file formats (.mgf, .msp, or .mzML) and need to convert them into a standardized bag-of-fragments representation for unsupervised topic modeling or substructure discovery workflows.
    0 installs
55. ▌
    Mass Spectrometry Metadata Extraction · holobiomicslab

    Use when you have peak/feature tables from one or more of MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to integrate them into a unified lipidomics workflow (e.g., LipidMatch).
    0 installs
56. ▌
    Mass Spectrometry Metadata Validation · holobiomicslab

    Use when after importing raw LC-MS/MS data files into the SIRIUS Java framework, before constructing indexed spectrum objects or submitting data to CSI:FingerID, CANOPUS, or MSNovelist web services.
    0 installs
57. ▌
    Mass Spectrometry Package Integration · holobiomicslab

    Use when you have R Spectra objects and need to apply Python-only MS algorithms (e.
    0 installs
58. ▌
    Mass Spectrometry Peak Classification · holobiomicslab

    Use when you have raw mzML files and feature tables (CSV format from mzMine or XCMS) from untargeted LCMS experiments and need to distinguish true metabolite peaks from false positives introduced by the peak-picking algorithm.
    0 installs
59. ▌
    Mass Spectrometry Prediction Modeling · holobiomicslab

    Use when when you have a collection of compound structures in SDF format (e.
    0 installs
60. ▌
    Metabolite Abundance Drift Correction · holobiomicslab

    Use when you have a raw LCMS nontargeted metabolomics abundance table spanning multiple injections with embedded pooled technical replicate (PREF) or internal standard injections distributed across the run sequence.
    0 installs
61. ▌
    Metabolite Pathway Annotation Mapping · holobiomicslab

    Use when after peak detection and statistical association or classification analysis has identified a set of significant peaks, use this skill when you need to move from individual feature-level results (peak intensities, p-values, importance scores) to functional biological interpretation via.
    0 installs
62. ▌
    Metabologenomic Database Construction · holobiomicslab

    Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified peptides (RiPPs) by integrating genomic and mass spectrometry data.
    0 installs
63. ▌
    Metabolomic Data Structure Formatting · holobiomicslab

    Use when after peak detection in MZmine2 has produced an MGF file (containing MS1 and MS2 spectra) and a feature abundance table (CSV or BIOM), but before running q2-qemistree tree construction or any QIIME 2-based metabolomic analysis.
    0 installs
64. ▌
    Metabolomic Feature Tree Construction · holobiomicslab

    Use when when you have preprocessed LC-MS/MS data (MGF file with MS1 and MS2 spectra and a feature abundance table from MZmine2 or similar peak detection tool) and need to perform chemical phylogeny-based diversity analyses or meta-analyses comparing metabolomic profiles across multiple samples or.
    0 installs
65. ▌
    Metabolomics Dataset Handling Massive · holobiomicslab

    Use when you are beginning a non-targeted metabolomics analysis and need to source raw LC-MS/MS data files (in mzML or NetCDF format) that have been vetted for quality and are known to support FBMN and statistical analysis.
    0 installs
66. ▌
    Metabolomics Feature Matrix Filtering · holobiomicslab

    Use when you have an aligned MemoMatrix (sample-by-feature occurrence matrix where features are MS2 peaks and neutral losses) and need to remove background noise before applying visualization or clustering techniques (MDS/PCoA, TMAP, Heatmap).
    0 installs
67. ▌
    Metabolomics Training Set Preparation · holobiomicslab

    Use when when you have LC-MS/MS acquisitions in DDA mode and need to train a customized DNMS2Purifier model to purify chimeric MS/MS spectra specific to your experimental conditions, metabolite classes, or ionization settings.
    0 installs
68. ▌
    Metadata Harmonization Across Sources · holobiomicslab

    Use when you have completed independent batch searches across one or more domain-specific MASST tools (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and received multiple separate output files (_microbe.html, _plant.json, _matches.tsv, _library.tsv, _datasets.tsv, _count_domain.
    0 installs
69. ▌
    Missing Pattern Generation Validation · holobiomicslab

    Use when you have a complete metabolomics data matrix (simulated or real abundance table) and need to create reproducible, controlled MNAR scenarios for evaluating imputation algorithm performance.
    0 installs
70. ▌
    Molecular Formula Parsing From Smiles · holobiomicslab

    Use when you have a query MS/MS spectrum with a SMILES string and adduct type (e.g., '[M+H]+', '[M+Na]+'), and you need to validate fragment ions against chemically plausible losses from the parent compound.
    0 installs
71. ▌
    Molecular Weight Inference Comparison · holobiomicslab

    Use when after RAMClustR clustering of XCMS-detected features and prior to final compound annotation, when you need to verify the robustness of molecular weight inference or when findMain and RAMClustR predictions are available for the same compound clusters and you want to assess concordance or.
    0 installs
72. ▌
    Mpactr Data Object Lifecycle Tracking · holobiomicslab

    Use when when chaining multiple mpactr filters on a peak table and you need to decide whether to preserve intermediate filtered objects or accept in-place mutation for memory efficiency.
    0 installs
73. ▌
    Mrm Transition Lipid Identity Mapping · holobiomicslab

    Use when after parsing raw MRM data into a transition table containing m/z values, retention times, and transition parameters.
    0 installs
74. ▌
    Msi Data Matrix Import And Validation · holobiomicslab

    Use when you have MSI intensity data exported from MSiReader, SCiLS, or Cardinal as plain-text CSV files or as Cardinal MSProcessedImagingExperiment/MSContinuousImagingExperiment objects, and need to load it into R as a validated msimat object for mass difference and adduct analysis.
    0 installs
75. ▌
    Multi Group Comparison Interpretation · holobiomicslab

    Use when after performing an ANOVA-style multi-group de_design() analysis on a LipidomicsExperiment object, when you need to determine whether a categorical sample variable (e.g., Cancer Stage, SampleType, Race) significantly associates with the lipid molecular profile.
    0 installs
76. ▌
    Multi Head Attention Mechanism Design · holobiomicslab

    Use when when building a transformer-based model to process mass spectrometry data (MS/MS spectra or fingerprints) where you need the model to learn multiple independent attention patterns across spectrum features simultaneously.
    0 installs
77. ▌
    Multidimensional Coordinate Alignment · holobiomicslab

    Use when you have detected feature tables from two or more LC-IMS-MS/MS samples (each containing m/z, drift_time, retention_time, and intensity measurements) and need to identify which features correspond to the same chemical compound across samples.
    0 installs
78. ▌
    Mzmine Batch Processing Configuration · holobiomicslab

    Use when you have raw metabolomics data in mzML or mzXML format and need to extract ion features, align them across samples, and produce a normalized feature table for downstream statistical or chemotaxonomic analysis.
    0 installs
79. ▌
    Natural Isotope Abundance Propagation · holobiomicslab

    Use when you have LC-MS fractional abundances of measured isotopologues (FAM) from a stable isotope labeling experiment and need to recover the true mass distribution vectors (MDV) that reflect only the contribution from the isotopic tracer. Use this skill when naturally occurring isotopes (e.
    0 installs
80. ▌
    Neural Network Threshold Optimization · holobiomicslab

    Use when after training a NeatMS neural network model on labelled peak data (High_quality, Low_quality, Noise) and you need to determine the optimal probability threshold for classifying peaks in your untargeted LCMS dataset.
    0 installs
81. ▌
    Noise Filtering Threshold Application · holobiomicslab

    Use when when you have raw or centroid-mode LC-MS All-ion fragmentation (AIF) spectra and need to generate or match against ion fragment databases.
    0 installs
82. ▌
    Non Pathway Metabolite Classification · holobiomicslab

    Use when you have metabolomics intensity data with peak annotations, and you want to rank and prioritize metabolite groupings (Molecular Families, Mass2Motifs, or other non-pathway metabolite sets) by their activity levels across experimental contrasts.
    0 installs
83. ▌
    Notification Configuration Management · holobiomicslab

    Use when setting up a Rapid QC-MS monitoring job and you need to define WHERE and HOW QC-fail alerts should be sent.
    0 installs
84. ▌
    Peak Intensity Threshold Optimization · holobiomicslab

    Use when you have loaded raw mass spectrometry spectral data (in MGF, MSP, mzML, or mzXML format) and need to decide which intensity threshold(s) to use for filtering out noise and low-abundance peaks.
    0 installs
85. ▌
    Peak Picking Performance Benchmarking · holobiomicslab

    Use when when you have completed non-targeted peak picking and alignment with tools such as MZmine 2, XCMS, or MS-DIAL on LC-HRMS mzML data and need to quantify performance metrics (found peaks %, degenerated isotopologue ratio, alignment errors) by comparing against a curated benchmark of known.
    0 installs
86. ▌
    Peak Property Dictionary Construction · holobiomicslab

    Use when when you have identified the set of analytes (peptides, nucleosides, or other biomolecules) you wish to simulate in silico, and you need to prepare their chemical properties (m/z, intensity, retention time) in a machine-readable format before applying fragmentation and noise injection.
    0 installs
87. ▌
    Peptide Isotopic Envelope Calculation · holobiomicslab

    Use when you have a peptide sequence, precursor charge state, and observed m/z spectrum and need to generate the expected isotopic distribution to match against observed precursor or fragment ion peaks. This is especially critical in SIP workflows where incorporation probabilities (e.g., 0.
    0 installs
88. ▌
    Precursor Ion Chromatogram Extraction · holobiomicslab

    Use when you have raw DIA mass spectrometry data files (.raw, .d, or .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to extract precursor ion chromatograms for quality assessment or downstream analysis.
    0 installs
89. ▌
    Precursor Mass Difference Calculation · holobiomicslab

    Use when when comparing two MS/MS spectra using modified cosine similarity and the precursor m/z values differ, indicating potential neutral losses, adduct variations, or analogs with different substituents.
    0 installs
90. ▌
    Precursor Peak Removal Mass Tolerance · holobiomicslab

    Use when after loading an MsmsSpectrum object but before intensity filtering or spectral annotation.
    0 installs
91. ▌
    R Bioconductor Workflow Orchestration · holobiomicslab

    Use when you have untargeted LC/MS metabolomics data from stable isotope labeling experiments (e.g., 13C-glucose vs. 12C-glucose) already converted to mzXML format, and you need to systematically identify putatively incorporated metabolic features by comparing unlabeled and labeled sample groups.
    0 installs
92. ▌
    R Python Interoperability Via Wrapper · holobiomicslab

    Use when you have a Spectra object in R and need to apply a specialized Python MS algorithm (e.
    0 installs
93. ▌
    Rc Object Construction And Validation · holobiomicslab

    Use when after feature detection and alignment (XCMS or equivalent), when you have a CSV feature table with m/z and retention time columns and need to group features derived from the same compound.
    0 installs
94. ▌
    Reaction Propensity Score Computation · holobiomicslab

    Use when you have measured intracellular metabolite abundances (LC-MS or similar) across multiple cell lines or conditions and a stoichiometric metabolic model (with reaction-metabolite associations) to estimate how differences in substrate availability—independent of gene expression—translate into.
    0 installs
95. ▌
    Redundant Feature Identification Lcms · holobiomicslab

    Use when after alignment of two or more same-method nontargeted LCMS datasets (e.g., via Eclipse) when you have a feature table containing retention times and feature intensities across samples. Use it when redundancy is expected—e.
    0 installs
96. ▌
    Relative Mass Defect Window Filtering · holobiomicslab

    Use when apply this filter when working with MS-DIAL peak lists (feature tables with m/z, retention time, and intensity) that contain features with anomalous mass defects—particularly when you have prior knowledge of the expected RMD range for your sample type or analytical method, or when you want.
    0 installs
97. ▌
    Retention Time And Mz Based Alignment · holobiomicslab

    Use when after peak detection has been completed on individual LC-MS samples and you have a collection of detected peaks with m/z, retention time, and intensity values from each sample.
    0 installs
98. ▌
    Retention Time Mapping Spline Fitting · holobiomicslab

    Use when after anchor feature pairs (m/z and retention time values) have been selected from two disparately-acquired LC-MS datasets, and you need to correct for systematic retention time differences between the datasets.
    0 installs
99. ▌
    Routing Module Testing And Validation · holobiomicslab

    Use when when you have implemented conditional routing logic in the GNPS_MASST codebase and need to verify that spectrum submissions with explicit domain-context selections (e.
    0 installs
100. ▌
     Scan Window Routing Mass Spectrometry · holobiomicslab

     Use when when processing LC-MS data with multiple overlapping m/z scan windows and observing sawtooth-pattern distortions in EICs during tardisPeaks() execution.
     0 installs