← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

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

1. ▌
   Chromatographic Modality Classification · holobiomicslab

   Use when when ingesting raw or vendor-format mass spectrometry data files of unknown or mixed acquisition modality, and you need to automatically determine whether the input originated from liquid chromatography (LC), gas chromatography (GC), ion mobility spectrometry (IMS), or MS imaging (e.
   0 installs
2. ▌
   Chromatographic Peak Overlap Resolution · holobiomicslab

   Use when analyzing GC-MS data containing overlapping chromatographic peaks—a common scenario in untargeted metabolomics and environmental screening where sample complexity or chromatographic resolution limitations cause co-elution of structurally similar or temporally proximate compounds.
   0 installs
3. ▌
   Chromatographic Retention Time Matching · holobiomicslab

   Use when you have GC-MS data with multiple replicate injections or samples, need to identify a predefined set of query chemicals by name, and want to consolidate all instances of those chemicals (which may appear with varying match factors or peak areas across different samples or injection.
   0 installs
4. ▌
   Ei Spectral Library Parsing And Merging · holobiomicslab

   Use when you need to build a comprehensive EI spectral reference library for GC-MS compound identification in MS-DIAL, starting from raw downloads of NIST, RIKEN, MoNA, or SWGDRUG libraries that have inconsistent metadata organization (SMILES in different fields or absent, RI values missing or.
   0 installs
5. ▌
   Injection Order Direction Specification · holobiomicslab

   Use when when configuring a multi-well plate design (96-well, 384-well, or other format) in InjectionDesign for LC/GC-MS analysis and you need to specify whether analytical samples and QC controls should be injected row-by-row or column-by-column.
   0 installs
6. ▌
   Mass Error And Retention Time Alignment · holobiomicslab

   Use when when processing low- or high-resolution mass spectrometry data (mzML profile or centroided format) for isotopologue quantification and you need to match detected peaks to a targeted formulaTable of compounds.
   0 installs
7. ▌
   Mass Spectrometry Spectrum Tokenization · holobiomicslab

   Use when you have pre-processed MS/MS spectra and need to prepare them for word-embedding-based similarity methods (e.g., Spec2Vec).
   0 installs
8. ▌
   Mass Spectrum Extraction And Formatting · holobiomicslab

   Use when you have raw GC-MS data in netCDF or vendor-specific binary format and need to separate co-eluting compounds and extract clean mass spectra for each individual chemical component prior to molecular networking, spectral matching, or metabolite identification workflows.
   2 installs
9. ▌
   Multi Dimensional Sample Stratification · holobiomicslab

   Use when you have a parsed sample list with metadata (sample IDs, classification dimensions, QC designations) and need to generate a physical injection-plate layout that (1) will be run across multiple batches, (2) has a known confounding dimension (e.
   2 installs
10. ▌
    Neutral Loss Calculation From Precursor · holobiomicslab

    Use when when converting MS/MS spectra into spectral documents for Spec2Vec embedding, and you want to capture chemical relationships implicit in the fragmentation pattern (e.g., loss of water, ammonia, or CO2) that may correlate with structural similarity. Use this when the neutral loss range (5.
    0 installs
11. ▌
    Peak Integration Parameter Optimization · holobiomicslab

    Use when after peak detection and clustering have been completed on aligned and baseline-corrected GC-IMS data, and before imputation or statistical analysis.
    2 installs
12. ▌
    Retention Index Calibration Application · holobiomicslab

    Use when when processing GC-MS data where retention time alone is insufficient for compound identification due to instrument drift or method variation, and you need to match detected peaks against a spectral library (e.
    1 install
13. ▌
    Retention Time Alignment Across Batches · holobiomicslab

    Use when you have extracted peaks from multiple LC/HRMS batches (n > 500 samples across different analytical runs or days) and observe systematic retention time drift or offset between batches, preventing reliable cross-batch peak matching on m/z and RT alone.
    2 installs
14. ▌
    Separation Technique Workflow Alignment · holobiomicslab

    Use when when evaluating whether an MS data processing platform (such as mzmine) supports the full range of separation/ionization techniques your laboratory uses, or when assessing whether gaps exist in the software architecture that would require external pre- or post-processing for specific.
    0 installs
15. ▌
    Signal Acquisition Error Quantification · holobiomicslab

    Use when you have processed the same GC–MS dataset (m/z vs retention time) through two independent signal acquisition pipelines and need to compute and compare their detection accuracy. Use this skill when one method (e.
    0 installs
16. ▌
    Spectral Similarity Scoring Computation · holobiomicslab

    Use when you have a query spectrum (or set of query spectra) and need to rank candidate library spectra by their likelihood of sharing the same chemical structure.
    0 installs
17. ▌
    Aif Spectrum Fragment Database Matching · holobiomicslab

    Use when you have a feature table from untargeted LC–MS all-ion fragmentation (AIF) chromatograms processed by xcms and RamClustR, and you want to assign metabolite annotations to individual features by comparing their experimental MS/MS spectra against curated fragment libraries (e.
    0 installs
18. ▌
    Bipartite Graph Maximum Weight Matching · holobiomicslab

    Use when you have two MS/MS fragmentation spectra with fragment ion lists and computed pairwise mass differences (m/z deltas) between them, and you need to find the alignment of ion pairs that: (1) does not reuse any ion from either spectrum, (2) maximizes total matching quality (e.
    1 install
19. ▌
    Candidate Metadata Record Serialization · holobiomicslab

    Use when after computing InChIKey and neighbourhood scores for library match candidates, you need to write results to a persistent format (CSV, JSON, or database) for storage, sharing, and interpretation.
    0 installs
20. ▌
    Changelog Maintenance And Documentation · holobiomicslab

    Use when you have added or modified user-facing parameters to a model class (such as L1/L2 regularization in SiameseModel), written unit tests to verify the new functionality, and need to communicate these changes to users and maintain a historical record.
    0 installs
21. ▌
    Chemical Structure Annotation Retrieval · holobiomicslab

    Use when you have MS/MS spectra from public repositories (e.g., GNPS) that lack chemical structure annotations (InChI/SMILES), or have incomplete/inconsistent annotations.
    0 installs
22. ▌
    Chromatogram Peak Matching Registration · holobiomicslab

    Use when you have multiple LC-MS samples in mzML or mzXML format with variable retention times, at least one designated as a quality control (QC) reference file, and you need to correct for RT drift before peak/feature detection.
    2 installs
23. ▌
    Chromatographic Peak Quality Assessment · holobiomicslab

    Use when when you have a feature table (CSV with m/z and retention time columns) and corresponding LC-MS raw data files (.mzXML or .mzML) from an untargeted metabolomics experiment, and need to filter out spurious peaks before downstream statistical or biological interpretation.
    0 installs
24. ▌
    Chunk Wise Data Processing Optimization · holobiomicslab

    Use when you have a large mass spectrometry dataset stored across multiple mzML, mzXML, or CDF files and need to perform operations (e.g., normalization, filtering, feature extraction) on the full dataset but memory constraints prevent loading all peak data simultaneously.
    0 installs
25. ▌
    CLI Invocation With File Path Arguments · holobiomicslab

    Use when you have vendor raw mass spectrometry data files (e.g., .raw, .d, .wiff2 formats) that must be converted to mzML or Aird format, and you need to automate the conversion in a batch workflow, Docker container, or non-interactive environment.
    2 installs
26. ▌
    Collision Cross Section Calibration Ccs · holobiomicslab

    Use when when you have acquired ion mobility–mass spectrometry data (drift time and m/z dimensions) and need to convert observed drift times into calibrated CCS values.
    0 installs
27. ▌
    Computational Environment Configuration · holobiomicslab

    Use when at the start of any DaDIA pipeline execution, or whenever you are preparing to run a complex multi-package R workflow on a new system or after updating package managers.
    0 installs
28. ▌
    Conformer Ensemble Generation Via Crest · holobiomicslab

    Use when you have a molecular geometry (XYZ format) and need to explore its conformational space prior to quantum mechanical property calculation or when QCxMS2 workflow requires an ensemble of low-energy structures to enable systematic fragmentation pathways for EI mass spectrum simulation.
    0 installs
29. ▌
    Consensus Classification Reconciliation · holobiomicslab

    Use when you have spectral features annotated by both in silico structural prediction tools (e.g., SIRIUS/CANOPUS) and spectral library matching (GNPS), and you need a single authoritative chemical classification per feature rather than a list of competing candidates.
    0 installs
30. ▌
    Correlation Cluster Network Integration · holobiomicslab

    Use when after identifying structural clusters (isotopologue groups, adduct groups, and cross-assay links) and assigning features to correlation clusters via hierarchical clustering.
    0 installs
31. ▌
    Cross Dataset Generalization Assessment · holobiomicslab

    Use when you have a pre-trained MS/MS spectral embedding model evaluated on one or more source datasets (GNPS, MoNA, MTBLS1572) and need to verify that it performs well on independent, high-quality curated spectral libraries to claim robustness.
    0 installs
32. ▌
    Cross Language Interface Implementation · holobiomicslab

    Use when you have a mature R analysis pipeline (e.g., using Spectra objects for MS data) but need access to specialized algorithms or calculations available only in Python libraries (e.g., CosineGreedy similarity from matchms).
    0 installs
33. ▌
    CSV Serialization For Mass Spectrometry · holobiomicslab

    Use when you have generated or curated a lipid spectral library (with precursor m/z, adduct information, charge states, retention times, and fragmentation patterns) and need to export it for use in either Excalibur-based DDA experiments on an Orbitrap mass spectrometer, or in Skyline for targeted.
    0 installs
34. ▌
    Dense Neural Network Layer Construction · holobiomicslab

    Use when when you have a binned MS/MS spectrum vector (e.g., 9948-dimensional input from 10,000 equally-spaced m/z bins in the 10–1000 Da range) and need to compress it into a learned latent representation (e.
    2 installs
35. ▌
    Distance Matrix Generation From Indexes · holobiomicslab

    Use when you have pre-computed feature-hashed spectrum vectors and nearest neighbor indexes constructed from those vectors, and you need a pairwise distance matrix as input to density-based clustering (e.g., DBSCAN).
    0 installs
36. ▌
    Duplicate Feature Detection And Removal · holobiomicslab

    Use when you have peak-picked LC-MS data with multiple features that may represent the same metabolite detected at slightly different m/z or retention time values due to instrument precision limits, isotope variants, or adduct forms.
    0 installs
37. ▌
    Entropy Search Algorithm Implementation · holobiomicslab

    Use when you need to search one or more query MS/MS spectra against large spectral libraries (hundreds of thousands to millions of spectra) and require real-time or near-real-time compound identification.
    2 installs
38. ▌
    False Positive Mitigation In Annotation · holobiomicslab

    Use when you have implemented an automated feature annotation or adduct detection module and need to verify that assigned labels (e.g., [M+NH4]+, [M+K]+, [M+H2O+H]+, [M-H2O+H]+) are accurate and do not produce erroneous assignments on a reference feature set.
    2 installs
39. ▌
    Fatty Acyl Chain Variant Identification · holobiomicslab

    Use when when a metabolite feature has been assigned a top-rank lipid annotation (e.g., LPC(14:0)) but you need to assess whether related lipid species containing the same fatty acyl chain(s) (e.g., PC fragments with 14:0 acyl chains) also match the observed spectrum with lower scores.
    0 installs
40. ▌
    Feature Missingness Threshold Filtering · holobiomicslab

    Use when after loading and formatting raw peak-picked LC-MS metabolomics data frames (via metabData constructor) when you need to eliminate features with poor sample coverage before feature alignment.
    0 installs
41. ▌
    Feature Similarity Network Construction · holobiomicslab

    Use when you have a filtered MS-DIAL peak list (post-generic filtering, containing m/z, retention time, and peak intensity metrics) and need to identify groups of co-eluting or structurally similar features before extracting parental signals or annotating metabolites.
    0 installs
42. ▌
    Feature Table Alignment And Integration · holobiomicslab

    Use when you have aligned feature tables (CSV format) paired with MS2 spectral data (MGF or mzML files) and need to compare chemodiverse samples with poor feature overlap or strong retention-time shifts across different LC methods or mass spectrometer technologies (e.g., Orbitrap vs. Q-ToF).
    0 installs
43. ▌
    Feature Table Blank Intensity Detection · holobiomicslab

    Use when after loading an MZmine3-exported feature quantification table from non-targeted LC-MS/MS data when your experiment includes blank (negative control) samples and you need to remove features attributable to contamination or instrument background before downstream statistical analysis.
    0 installs
44. ▌
    Feature Wise Spectrum Count Aggregation · holobiomicslab

    Use when when you have extracted concatenated MS/MS spectra for multiple features from replicate mzML files and need to verify that a TIC-based filtering step (e.g., top x% TIC extraction) reduces per-feature spectrum counts to expected target levels.
    0 installs
45. ▌
    Filter Outcome Aggregation And Counting · holobiomicslab

    Use when after applying one or more mpactr filters (mispicked, group, cv, insource) to a feature table, you need to quantify the distribution of ions by their pass/fail status across filters to understand filtering impact, identify potential over-filtering, or communicate QC results via treemap or.
    2 installs
46. ▌
    Formula Annotation Capping By Frequency · holobiomicslab

    Use when when preparing multi-formula MS/MS training data for a rescore model, if the raw positive examples show extreme imbalance (some formulas represented by hundreds of spectra while others have only a few).
    0 installs
47. ▌
    Formula Assignment In Mass Spectrometry · holobiomicslab

    Use when you have m/z values from mass spectrometry imaging (or similar MSI experiments) and need to assign molecular formulae to them. This is especially valuable when working with spatially-resolved metabolomics data where annotation precision lags behind traditional LC-MS approaches.
    0 installs
48. ▌
    Fragmentation Pattern Spectral Matching · holobiomicslab

    Use when when you have detected m/z values from LC-IM-MS/MS that match a candidate CCS prediction database but require structural confirmation. Apply this skill to disambiguate isomers (e.
    0 installs
49. ▌
    Gnps Data Format Conversion And Mapping · holobiomicslab

    Use when you have GNPS molecular networking output (from GNPS1 at https://gnps.ucsd.edu or GNPS2 at https://gnps2.org) that must be integrated with antiSMASH BGC data and MIBiG metadata for natural product mining.
    2 installs
50. ▌
    Graphical Time Warping Parameter Tuning · holobiomicslab

    Use when your XCMS-processed LC-MS dataset exhibits retention-time drift or misalignment artifacts—particularly when analyzing hundreds of samples, data acquisition spans longer than one week, or you observe feature groups with inconsistent m/z or RT that XCMS grouped under a single global warping.
    0 installs
51. ▌
    Instrument Agnostic Feature Engineering · holobiomicslab

    Use when you have DIA raw mass spectrometry files from multiple instrument types (timsTOF, TripleTOF, Orbitrap) and need to build a single machine learning model to predict data quality across all platforms, or when you need to compare quality characteristics of files produced by different.
    0 installs
52. ▌
    Interactive Plot Construction Mass Spec · holobiomicslab

    Use when after LC-MS data has been converted to mzML format and processed through peak detection (e.g., MS-DIAL output) to yield a feature table with internal standard identifications, retention times, m/z values, and intensity measurements across multiple samples.
    2 installs
53. ▌
    Ion Current Calculation And Aggregation · holobiomicslab

    Use when when raw LC-MS feature tables exhibit inter-sample intensity variation due to instrument sensitivity drift, sample ionization efficiency differences, or loading differences, and you need to normalize intensities to a common reference scale before downstream statistical analysis.
    2 installs
54. ▌
    Isotopologue Adduct Link Identification · holobiomicslab

    Use when you have selected statistically significant features from multi-assay untargeted LC-MS metabolomics data and need to group them by structural relationships defined by their mass-to-charge ratios (m/z) and retention times (RT).
    0 installs
55. ▌
    JSON Serialization Of Metabolomics Data · holobiomicslab

    Use when after pre-annotation grouping (e.g., via khipu) has assigned features to empirical compounds, or when exporting feature tables and metadata from asari for downstream analysis in MetaboAnalyst or custom R/Python workflows.
    0 installs
56. ▌
    K Fold Cross Validation Model Selection · holobiomicslab

    Use when when fitting a multi-block PLS discriminant model on multi-assay LC-MS metabolomics data and you need to determine the number of latent variables to retain without overfitting.
    0 installs
57. ▌
    Knowledge Data Driven Layer Integration · holobiomicslab

    Use when you have untargeted metabolomics data (MS/MS spectra) and need to annotate metabolites at scale.
    0 installs
58. ▌
    Lipid Derivatization Chemistry Modeling · holobiomicslab

    Use when you have N-methyl-derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict their MS/MS fragmentation behavior before experimental acquisition, or to build a reference spectral library for isomer-level sterol identification in tissue samples.
    0 installs
59. ▌
    Lipid Fragmentation Pattern Application · holobiomicslab

    Use when you have an enumerated list of lipid species (identified by class, fatty acid composition, and chain length) and need to generate theoretical precursor m/z values, fragment ion masses, and relative intensities for targeted or untargeted lipidomics experiments.
    0 installs
60. ▌
    Lipid Fragmentation Pattern Recognition · holobiomicslab

    Use when you have experimental tandem MS (MS/MS) spectra from lipid samples (in mzML format) and need to assign molecular identities and lipid classes.
    0 installs
61. ▌
    Mass Action Kinetics Propensity Scoring · holobiomicslab

    Use when you have intracellular metabolomics measurements (absolute metabolite abundances) for multiple biological samples and want to identify which metabolic reactions are controlled by substrate availability rather than gene expression.
    2 installs
62. ▌
    Mass Spectrometry Data Table Formatting · holobiomicslab

    Use when when you have raw or processed TWIM-MS data (arrival time and m/z values) from a mass spectrometry instrument and need to organize it into a feature table before biomolecular class assignment or CCS calculations.
    0 installs
63. ▌
    Mass Spectrometry Feature Deconvolution · holobiomicslab

    Use when you have a peak table from LC-MS peak picking software (e.
    0 installs
64. ▌
    Mass Spectrometry Feature Deduplication · holobiomicslab

    Use when immediately after MZmine feature detection when you have both MGF (MS/MS spectra) and CSV (metadata) output files for one or both ionization modes and wish to construct a deduplicated molecular network.
    0 installs
65. ▌
    Mass Spectrometry Structural Annotation · holobiomicslab

    Use when after identifying statistically significant features (e.
    0 installs
66. ▌
    Mass Spectrometry Tolerance Calibration · holobiomicslab

    Use when after generating a feature table from mzML data (via Asari) and before performing MS1 or MS2 annotation.
    2 installs
67. ▌
    Mass Spectrum Binning And Vectorization · holobiomicslab

    Use when when preparing MS/MS spectra for neural network training or inference, particularly when you need to feed variable-length spectra into a Siamese network or embedding model that requires fixed-dimensional input.
    0 installs
68. ▌
    Mass Spectrum Peak Manipulation Merging · holobiomicslab

    Use when after generating electronic noise (uniformly sampled m/z with Poisson-distributed intensities) and chemical noise (formula database-sampled m/z with Poisson intensities) and you need to combine both noise types with a clean baseline spectrum into a single unified peak array.
    0 installs
69. ▌
    Metabolite Feature Table Interpretation · holobiomicslab

    Use when immediately after executing the MetaboAnalystR 4.0 unified LC-MS workflow (feature detection and quantification module) on raw mzML or netCDF data.
    0 installs
70. ▌
    Metabolite Identifier Mapping To Lipids · holobiomicslab

    Use when you have (1) peak-picked LC-MS AIF features in a feature table with m/z and retention time, (2) corresponding xcmsSet and RAMClustR pseudo-MS/MS spectral objects from centroid-mode raw data, and (3) a research goal to identify which features are lipids rather than other metabolite classes.
    2 installs
71. ▌
    Metabolite Protein Network Construction · holobiomicslab

    Use when after generating metabolite-disease correlation data and protein association predictions from a deep learning metabolomics module (e.g., DeepMSProfiler's feature extraction step).
    0 installs
72. ▌
    Metabolomic Data Format Standardization · holobiomicslab

    Use when you have raw peak table data from liquid chromatography–mass spectrometry (LC-MS) or related metabolomic instruments, generated by one of 12 supported software tools (or already in NOREVA's standardized format), and need to prepare it for preprocessing method evaluation or biomarker.
    2 installs
73. ▌
    Metabolomics Data Integration With Xcms · holobiomicslab

    Use when you have untargeted LC-MS metabolomics data preprocessed with XCMS and need to filter out low-quality peak integrations that could introduce false positives or noise into metabolite quantification.
    0 installs
74. ▌
    Metabolomics Experiment Object Handling · holobiomicslab

    Use when when converting raw metabolomics data from external formats (tab-delimited text, Sciex OS exports) into a unified R analysis environment, or when you have an existing SummarizedExperiment from another pipeline (e.
    0 installs
75. ▌
    Metabolomics Feature Quality Assessment · holobiomicslab

    Use when after drift correction and before missing value imputation when your LC-MS peak table contains features with variable detection rates across samples.
    0 installs
76. ▌
    Metabolomics Npp Reliability Assessment · holobiomicslab

    Use when you have completed NPP runs from one or more metabolomics tools on a set of LC-HRMS mzML files AND you have reference information (target molecule list with molecular formula, main adduct, and RT boundaries) available for a subset of expected compounds in those files.
    0 installs
77. ▌
    Molecular Graph Representation Encoding · holobiomicslab

    Use when when you have a collection of molecular structures (as InChI strings, SMILES, or RDKit Mol objects) and need to feed them into a pretrained or transfer-learning neural network that expects both molecular graph topology and structural fingerprints as inputs.
    0 installs
78. ▌
    Molecular Graph Representation Learning · holobiomicslab

    Use when when you have molecular structures (SMILES or chemical graphs) from a database like PubChem and need to predict molecular properties (e.
    0 installs
79. ▌
    Molecular Network Metadata Organization · holobiomicslab

    Use when when you have a GNPS molecular networking task ID (from GNPS1 or GNPS2 workflows: METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING, classical_networking_workflow, or feature_based_molecular_networking_workflow) and need to prepare the job archive for NPLinker.
    0 installs
80. ▌
    Motif Similarity Ranking Interpretation · holobiomicslab

    Use when after executing MassQL queries against a MotifDB reference database and retrieving ranked motif matches, when you need to determine which database entries represent true structural correspondence versus spurious matches, and to decide whether a motif's top-ranking hit is sufficiently.
    2 installs
81. ▌
    Ms Dial Feature Detection And Alignment · holobiomicslab

    Use when when you have raw LC-HRMS data in .mzML or .abf format and need to detect metabolite features (peaks) across multiple samples, align them temporally and by mass-to-charge ratio, and generate a reproducible feature matrix.
    0 installs
82. ▌
    Ms Ms Spectrum Annotation Preprocessing · holobiomicslab

    Use when you have raw LC-MS/MS data acquired in Data-Dependent Acquisition (DDA) mode and need to create a labeled training dataset for customized purification model development.
    0 installs
83. ▌
    Ms Spectrum Filtering And Normalization · holobiomicslab

    Use when you have raw or parsed tandem MS spectra (MGF, mzML, or in-memory Spectrum objects) and need to remove artifacts and normalize intensities prior to spectral matching, library searching, or downstream analysis.
    0 installs
84. ▌
    Transformation Product Parent Linkage · holobiomicslab

    Use when after suspect screening has identified both parent features (from before-treatment or reference samples) and TP candidate features (from after-treatment or exposed samples) in the same analysis set, and you have MS/MS spectral data or formula annotations available.
    0 installs
85. ▌
    Transformer Encoder Decoder Inference · holobiomicslab

    Use when when you have preprocessed MS/MS spectra (normalized intensities, filtered for quality, with top peaks retained) that have been encoded using a spectral representation method (e.
    2 installs
86. ▌
    Transient Window Function Application · holobiomicslab

    Use when when processing raw FT-ICR transient files (Bruker Solarix .d format or equivalent) intended for high-resolution mass spectral analysis.
    0 installs
87. ▌
    Unit Test Design For Model Parameters · holobiomicslab

    Use when you have extended a neural network model class (e.
    0 installs
88. ▌
    Algorithm Parameter Comparison Analysis · holobiomicslab

    Use when when you need to evaluate how a specific algorithm parameter (such as SearchMolecularFormulas first_hit mode) affects the quantity and quality of molecular formula assignments on a given spectrum or dataset.
    0 installs
89. ▌
    Candidate Formula Ranking By Mass Error · holobiomicslab

    Use when after querying a formula database (KEGG, PubChem, or user-supplied) with neutral mass values derived from observed m/z peaks and adduct transformations, when multiple candidate formulae fall within the configured mass tolerance window (ppm or Da) and you need to rank them by likelihood.
    0 installs
90. ▌
    Data Normalization In Mass Spectrometry · holobiomicslab

    Use when you have raw or partially processed metabolomics data (mzML/mzXML format) from LC-MS or GC-MS runs and need to apply standardized feature detection, alignment, and intensity normalization as part of a reproducible workflow.
    2 installs
91. ▌
    Fda Repeatability Compliance Assessment · holobiomicslab

    Use when you have completed NMR data quality control analysis and possess per-feature CV values, and you need to formally assess whether the metabolomic dataset meets FDA regulatory standards for downstream biomarker discovery or quantitative assays.
    2 installs
92. ▌
    Metabolite Prediction Pathway Selection · holobiomicslab

    Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to predict its metabolic fate across one or more biological systems.
    0 installs
93. ▌
    Nmr Peak Prediction Via Database Lookup · holobiomicslab

    Use when you have extracted peak data (chemical shift values in ppm, multiplicities, integration) from a processed NMR spectrum (JCAMP, RAW, or mzML format) and need to match these peaks against known NMR signals to propose or confirm structural assignments.
    0 installs
94. ▌
    Peak List Filtering For Quality Control · holobiomicslab

    Use when you have extracted a raw peak list (chemical shifts in a TXT file, one per row) from a 1D 1H NMR spectrum and intend to pass it to NMRformer or a similar deep learning model for metabolite identification.
    0 installs
95. ▌
    Qc Coefficient Of Variation Calculation · holobiomicslab

    Use when after extracting NMR spectra and designating replicate QC samples (typically 10 samples run throughout the study), calculate CV for each metabolite feature to assess which signals are reproducible enough for downstream metabolite-phenotype association testing.
    2 installs
96. ▌
    Tabular Data Transformation With Pandas · holobiomicslab

    Use when when converting mwTab-formatted metabolomics files (containing MS/NMR tabular data blocks) to JSON, or when you need to extract, manipulate, and re-serialize tabular sections from mwTab files while maintaining column structure and type information.
    0 installs
97. ▌
    Tensorflow Serving Endpoint Integration · holobiomicslab

    Use when you have nuclear magnetic resonance (NMR) peak data (1H and 13C measurements) that you need to classify using a deployed SMART 3 model, and you want to submit peaks programmatically rather than through a web UI.
    0 installs
98. ▌
    Atac Seq Feature Matrix Construction · holobiomicslab

    Use when when you have processed scATAC-seq data (peak calling complete, cell-barcode matrix generated) and need to register it into ArchR for downstream multiome analysis alongside scRNA-seq gene expression data.
    0 installs
99. ▌
    Bed Format Generation From Dataframe · holobiomicslab

    Use when you have extracted quantitative genomic features (e.g., insulation scores, boundary annotations) as a pandas DataFrame with bin coordinates and boolean or numeric columns, and need to export them as BED format for visualization in genome browsers (e.
    0 installs
100. ▌
     Binary Path Detection And Validation · holobiomicslab

     Use when when setting up a bioinformatics pipeline (particularly Hi-C data processing) that depends on multiple external binaries with version constraints, and you need to configure the environment in a way that is both portable across systems and reproducible across runs.
     1 install