← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 7.4k skills
• 0 followers
• 1 day ago last updated

1. ▌
   Isotopic Enrichment Simulation · holobiomicslab

   Use when you have a peptide sequence and need to predict its theoretical m/z values under partial or complete isotopic enrichment (e.g., 1% natural 13C abundance, 50% 13C labeling, or other SIP conditions).
   0
   installs
2. ▌
   Lc Ms Adduct Pattern Detection · holobiomicslab

   Use when when you have statistically significant features from multi-assay LC-MS metabolomics data (with m/z and retention time annotations) and need to group features that may represent the same compound ionized as different adducts (e.g., [M+H]⁺ vs. [M+Na]⁺).
   0
   installs
3. ▌
   Lc Ms Peak Feature Engineering · holobiomicslab

   Use when you have LC-MS feature tables with m/z and retention time coordinates paired with raw .mzXML or .mzML data files, and you need to systematically assess which features correspond to genuine chromatographic peaks versus noise or artifacts.
   0
   installs
4. ▌
   Lda Model Training Convergence · holobiomicslab

   Use when you have a preprocessed bag-of-fragments corpus derived from tandem mass spectrometry spectra and need to discover recurring fragmentation motifs without prior compound identification.
   0
   installs
5. ▌
   Link Scoring Metcalf Algorithm · holobiomicslab

   Use when you have loaded GCFs (from AntiSMASH via BigScape clustering), GNPS spectra, and molecular families (from GNPS molecular networking), and need to compute pairwise scoring between genomic and metabolomic entities to identify putative gene cluster–metabolite associations.
   0
   installs
6. ▌
   Mass Spectral Feature Grouping · holobiomicslab

   Use when you have untargeted metabolomics MS/MS spectra from multiple features and need to identify which features belong to the same molecular family or are related by biotransformation.
   0
   installs
7. ▌
   Mass Spectrometry Data Loading · holobiomicslab

   Use when you have raw MS data files from supported instruments (Agilent, Thermo, Bruker, or mzML format) and need to ingest them into IonToolPack for visualization, quality control, targeted extraction, or spectral library matching.
   0
   installs
8. ▌
   Mass Spectrum De Novo Analysis · holobiomicslab

   Use when you have an unknown MS/MS spectrum (m/z and intensity pairs) from positive-mode ionization and need to identify the most likely molecular formula and adduct type (e.g., [M+H]+, [M+Na]+) when no reference library match is available or desirable.
   0
   installs
9. ▌
   Metabolights Dataset Retrieval · holobiomicslab

   Use when you have a MetaboLights dataset identifier (e.g., MTBLS1124) and need to download a specific mzML file (e.g., QC07.mzML) from the public repository for visualization, quality control assessment, or integration into a metabolomics workflow. The USI format mzspec:MTBLS1124:QC07.
   0
   installs
10. ▌
    Metabolite Annotation At Scale · holobiomicslab

    Use when you have extracted a large feature set of m/z values (hundreds to tens of thousands) from a Cardinal MSImagingExperiment object or similar MS dataset and need to assign putative metabolite identities using public structural databases.
    0
    installs
11. ▌
    Metabolite Intensity Alignment · holobiomicslab

    Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE method (high-pressure liquid chromatography–mass spectrometry output) and need to prepare them for multivariate analysis to detect differential lipids and metabolites across biological samples (e.
    0
    installs
12. ▌
    Metabolomics Sample Comparison · holobiomicslab

    Use when you have a MemoMatrix (sample-by-fingerprint matrix) from aligned MS2 spectra and need to visually compare sample similarity or clustering patterns, especially when samples show poor feature overlap, strong retention time shifts across different LC methods, or were acquired on different.
    0
    installs
13. ▌
    Ms Dial Export Format Handling · holobiomicslab

    Use when you have performed lipid identification in MS-DIAL and need to pass the results to LipoCLEAN or another downstream quality-filtering tool. The skill is required whenever you are preparing MS-DIAL output for consumption by external analysis pipelines that expect standardized export formats.
    0
    installs
14. ▌
    Ms Ms Spectrum Peak Annotation · holobiomicslab

    Use when you have an experimental MS/MS spectrum (e.g., from MassBank or local data) and need to identify significant fragment ions above noise, assign occurrence scores to peaks, and generate a CSV-formatted library entry for use in metabolite feature annotation pipelines.
    0
    installs
15. ▌
    Ms2 Fingerprint Matrix Merging · holobiomicslab

    Use when you have two MemoMatrix objects generated from separate sample cohorts (e.
    0
    installs
16. ▌
    Ms2lda Substructure Assignment · holobiomicslab

    Use when you have a GNPS molecular network (in GML or GraphML format) and a completed MS2LDA experiment on ms2lda.org, and you want to annotate network nodes with detected substructural motifs to identify shared fragmentation patterns and structural classes across molecular families.
    0
    installs
17. ▌
    Multi Class Network Annotation · holobiomicslab

    Use when you have (1) metabolite-disease correlation matrices and protein association predictions generated by a deep learning module (e.
    0
    installs
18. ▌
    Multi Panel Spectra Comparison · holobiomicslab

    Use when when you need to visually compare two or more spectra (MS1, MS2, or extracted ion chromatograms) across different retention times, m/z ranges, or ion mobility bins in a single figure. Apply this skill after extracting spectra arrays from MZA files (e.
    0
    installs
19. ▌
    Multi Sample Cohort Assessment · holobiomicslab

    Use when when you have MS1 mass spectrometry data from multiple samples (a cohort) acquired across an instrument run or batch, and you need to identify which samples deviate from cohort norms or which ion targets show anomalous behavior.
    0
    installs
20. ▌
    Multi Species Lipid Prediction · holobiomicslab

    Use when you have candidate lipid annotations from high-throughput spectral matching (e.
    0
    installs
21. ▌
    Neural Network Scoring Ranking · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (m/z and intensity pairs), a set of candidate chemical formula–adduct pairs (enumerated via SIRIUS or another generator), and need to rank them by credibility without access to a spectrum library.
    0
    installs
22. ▌
    Nextflow Profile Customization · holobiomicslab

    Use when you need to execute a Nextflow metabolomics workflow (e.
    0
    installs
23. ▌
    Outlier Feature Classification · holobiomicslab

    Use when after peak picking by MS-DIAL and import into R, when the feature table contains m/z values with decimal components that fall within the [4, 8] interval (indicating instrumental artifacts or calibration errors).
    0
    installs
24. ▌
    Peak And Neutral Loss Counting · holobiomicslab

    Use when when you have matchms-processed MS2 spectra from multiple samples and need to create comparable sample-level signatures for cross-sample analysis, particularly when samples are chemodiverse, have poor feature overlap, or exhibit strong retention time shifts across LC methods or MS.
    0
    installs
25. ▌
    Qc Summary Table Extraction · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, call qc_summary() to obtain a structured report of which ions passed or failed each filter.
    0
    installs
26. ▌
    R6 Object Method Invocation · holobiomicslab

    Use when when working with large metabolomics peak tables (e.
    0
    installs
27. ▌
    Repository Backend Dispatch · holobiomicslab

    Use when when you have a USI string (e.g., 'mzspec:GNPS:TASK-abc123:scan:1943') and need to retrieve the underlying spectrum data from its native repository without knowing a priori which backend stores it.
    0
    installs
28. ▌
    Repository Code Integration · holobiomicslab

    Use when you have identified a published method (e.g., MIST-CF for chemical formula ranking from mass spectra) whose source code and trained weights are available in a public repository, and you need to apply that method to new experimental data (e.
    0
    installs
29. ▌
    Retention Time Mz Alignment · holobiomicslab

    Use when processing raw LC/MS data (mzML or mzXML format) from multi-sample cohorts where retention time or intensity drift is suspected due to batch effects, instrument calibration drift, or variable run order.
    0
    installs
30. ▌
    Retention Time Scan Mapping · holobiomicslab

    Use when when you have loaded an LC-MS spectrum file (mzML, mzXML, or equivalent) into the GNPS LCMS Visualization Dashboard and need to annotate extracted ion chromatograms with the precise retention time or scan ID positions where MS2 events occurred.
    0
    installs
31. ▌
    Sample Metadata Integration · holobiomicslab

    Use when when you have LC-MS peak table data in Excel format (e.g., from MS-DIAL peak picking) with separate compartments for sample information, feature properties, and intensity values, and you need to construct a structured R object that enforces consistency between sample metadata (e.
    0
    installs
32. ▌
    Scoring Module Unit Testing · holobiomicslab

    Use when after implementing or modifying the scoring module that computes average InChIKey scores and neighbourhood scores for candidate matches, or when integrating new scoring logic into an existing MS2Query pipeline.
    0
    installs
33. ▌
    Snr Based Signal Validation · holobiomicslab

    Use when after composite map peak detection has generated a full unfiltered peak list with SNR values computed for each candidate peak.
    0
    installs
34. ▌
    Spec2vec Similarity Scoring · holobiomicslab

    Use when after discovering Mass2Motifs via LDA on preprocessed MS/MS spectra, use this skill to assign putative substructure annotations by matching each motif's fragmentation pattern against a pre-indexed spectral library using learned spectral embeddings.
    0
    installs
35. ▌
    Spectral Data Serialization · holobiomicslab

    Use when after completing MS/MS spectra detection and peak recognition on tandem MS breath samples.
    0
    installs
36. ▌
    Spectral Data Visualization · holobiomicslab

    Use when you have executed MassQL queries on mzML mass spectrometry data and need to communicate query results visually—particularly when comparing peak shapes across multiple files, assessing retention time distributions, or validating precursor/product ion matches.
    0
    installs
37. ▌
    Spectral Mz Range Filtering · holobiomicslab

    Use when you have loaded an MsmsSpectrum object from a proteomics or metabolomics dataset and need to focus the analysis window on a specific m/z range relevant to your experiment (e.g., 100–1400 m/z for typical tryptic peptides).
    0
    installs
38. ▌
    Spectral Peak Visualization · holobiomicslab

    Use when you have a resolved mass spectrum (m/z values, intensities, and metadata) from a supported USI source (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA, or MassIVE) and need to create a publication-ready image that retains a link back to an interactive spectrum.
    0
    installs
39. ▌
    Spectral Similarity Ranking · holobiomicslab

    Use when you have a query MS/MS spectrum and need to identify the -matching library spectrum from a large spectral database, particularly when the research goal requires distinguishing between exact matches and structural analogues without separate workflows.
    0
    installs
40. ▌
    Spectrum Cluster Assignment · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters. Use this skill when: (1) you have a sparse similarity or distance matrix as input;
    0
    installs
41. ▌
    Tabular Data Io And Masking · holobiomicslab

    Use when after generating a preliminary feature table from LC-MS data (e.g., via Asari), when experimental design includes blank samples or negative controls and you need to filter out features that are likely instrumental or chemical background rather than true biological signal.
    0
    installs
42. ▌
    Tic Based Intensity Scaling · holobiomicslab

    Use when after feature detection when you have a metabolomics feature table with intensity values across multiple samples and observe evidence of inter-sample intensity bias (e.g., batch effects, variable ionization efficiency, or instrument drift).
    0
    installs
43. ▌
    Tree Based Model Validation · holobiomicslab

    Use when after training a decision tree classifier on ChemEcho sparse feature vectors (representing tandem mass spectra fragmentation patterns), especially when the goal is to deploy predictions as executable queries or to validate that learned splits correspond to chemically meaningful.
    0
    installs
44. ▌
    Uhplc Hrms Ms Data Matching · holobiomicslab

    Use when you have peak-picked UHPLC-HRMS/MS data (from Q-Exactive orbitrap, Agilent, Bruker, or SCIEX Q-TOF instruments) with both MS1 and MS/MS fragment spectra, and you need to assign lipid identities to detected features using in-silico fragmentation patterns.
    0
    installs
45. ▌
    Web Service API Integration · holobiomicslab

    Use when when you have a parsed mass spectrum (precursor m/z, ionization mode, collision energy, and fragment peak list as m/z–intensity pairs) and need to obtain molecular fingerprint predictions, de-novo candidate structures, or chemical class annotations without maintaining local neural network.
    0
    installs
46. ▌
    YAML Configuration Handling · holobiomicslab

    Use when when initializing a MolNotator project with user-defined parameters for ionization modes, adduct tables, database selections, output directories, and tool-specific thresholds.
    0
    installs
47. ▌
    Annotation Confidence Scoring · holobiomicslab

    Use when after recursive annotation propagation has assigned metabolite labels to previously unannotated nodes in a two-layer metabolomic network, and before reporting final annotated metabolite identities.
    0
    installs
48. ▌
    API Request Response Handling · holobiomicslab

    Use when you have nuclear magnetic resonance (NMR) peak data (proton 1H and carbon-13 13C measurements) that you need to classify using a deployed deep learning model, and you have access to a TensorFlow Serving instance running the SMART 3 classification model.
    0
    installs
49. ▌
    Array Of Objects Construction · holobiomicslab

    Use when you have tabular experimental data (e.g., sample metadata, mass spectrometry parameters, NMR acquisition details) in JSON table format and need to produce a list of structured objects for submission to a data repository (e.g., Metabolomics Workbench) or downstream format conversion.
    0
    installs
50. ▌
    Dependency Version Management · holobiomicslab

    Use when when you need to document or reproduce a Python-based research application (or any package-dependent workflow) and discover that the original publication or repository specifies dependencies without versions, or when you want to verify that a documented set of pinned versions can be.
    0
    installs
51. ▌
    Form Encoded Request Handling · holobiomicslab

    Use when when a web service must accept spectroscopic measurements (NMR peaks, IR/MS metadata) submitted as form-encoded POST parameters from a client, and those parameters need to be validated, reformatted into an external API query format, or passed to a downstream predictor service.
    0
    installs
52. ▌
    Mass Spectral Data Validation · holobiomicslab

    Use when you have raw LC-MS/MS spectral data in vendor formats or unvalidated .mgf files before feeding them into the specXplore importing pipeline.
    0
    installs
53. ▌
    Minimum Cost Flow Formulation · holobiomicslab

    Use when you have an NMR mixture spectrum and a library of single-compound reference spectra, and you need to identify which compounds are present and their relative abundances.
    0
    installs
54. ▌
    Nmr Spectrum Phase Adjustment · holobiomicslab

    Use when you have acquired raw 1D NMR spectra (FID or processed spectra in NMRPipe format) that exhibit phase distortion—where peaks are not in pure absorption mode—and you need to prepare the spectrum for automatic deconvolution into peak tables.
    0
    installs
55. ▌
    Nmrbox Environment Management · holobiomicslab

    Use when when you need to deploy SAND for 1D NMR spectrum deconvolution on a new machine or cluster, or when testing code changes before merging into production.
    0
    installs
56. ▌
    Quality Metrics Summarization · holobiomicslab

    Use when after running QC analysis on NMR or MS metabolomic data and obtaining per-feature CV values, use this skill to validate that the dataset meets FDA thresholds (CV < 0.30 for discovery, CV < 0.15 for quantification) and to report the proportion of features meeting each threshold.
    0
    installs
57. ▌
    Record Grouping And Collation · holobiomicslab

    Use when you have multiple rows in a table that describe the same logical entity (e.g., multiple measurements from the same sample, or repeated attributes under a common identifier) and need to merge them into a single dictionary entry keyed by that shared field.
    0
    installs
58. ▌
    Spectral Graph Interpretation · holobiomicslab

    Use when after submitting MS/MS data and feature tables to GNPS and receiving a molecular networking job result.
    0
    installs
59. ▌
    450k Array Data Processing · holobiomicslab

    Use when you have raw .idat files or beta-valued matrices from HumanMethylation450 (450k) arrays and need to remove low-quality probes, correct for technical artifacts (batch effects, type-2 probe bias), and normalize the data before performing differential methylation analysis or DMR detection.
    0
    installs
60. ▌
    Archr Project Manipulation · holobiomicslab

    Use when you have a processed ArchR project object (containing peak calls, cell barcodes, and quality control metadata) and need to: (1) reduce dimensionality of the peak matrix via iterative LSI; (2) integrate multimodal data by combining ATAC and RNA dimensions;
    0
    installs
61. ▌
    Atac Seq Footprint Scoring · holobiomicslab

    Use when you have completed Tn5 insertion bias correction on ATAC-seq reads and now need to quantify footprint signal strength (signal depletion around TF-bound sites) across accessible chromatin regions before classifying individual TF binding sites.
    0
    installs
62. ▌
    Methylbase Object Handling · holobiomicslab

    Use when after reading in per-sample methylation call files with methRead() and obtaining methylRawList objects, but before calculating differential methylation or performing annotation.
    0
    installs
63. ▌
    Tsv File Io And Formatting · holobiomicslab

    Use when you have computed or received a precomputed expected contact frequency table (e.
    0
    installs
64. ▌
    Arrow Table Serialization · holobiomicslab

    Use when you have loaded mzPeak spectrum or chromatogram metadata and signal data into PyArrow Table structures (via the Python mzPeak reader or equivalent) and need to persist them to disk in Parquet format for downstream analysis, interoperability with other languages (R, .
    0
    installs
65. ▌
    CI CD Pipeline Monitoring · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as a Build and Publish pipeline) executes successfully on a specific branch (e.g., release branch) and produces a passing build status.
    0
    installs
66. ▌
    CI CD Workflow Monitoring · holobiomicslab

    Use when when you need to verify that a continuous integration pipeline for a scientific software project (e.g., mzmine) completes successfully, produces expected build artifacts, or fails in a reproducible manner.
    0
    installs
67. ▌
    CI CD Workflow Triggering · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that automated build infrastructure is functioning correctly.
    0
    installs
68. ▌
    Descriptor Table Assembly · holobiomicslab

    Use when when you have calculated molecular descriptors from validated chemical structures and need to prepare them for BitterPredict.m classification. Use this skill after descriptor calculation is complete and before invoking BitterPredict.m for bitter/non-bitter predictions.
    0
    installs
69. ▌
    Expert Review Preparation · holobiomicslab

    Use when you have a published scientific article describing a computational method (e.g., natural products annotation, MS/MS data processing) and need to assess reproducibility before expert scrutiny.
    0
    installs
70. ▌
    Feature Ablation Analysis · holobiomicslab

    Use when when you have a trained GNN model for molecular property prediction (e.g., collision cross section) and need to identify which graph structural features—atomic properties, bond types, or higher-order graph descriptors—are driving the model's predictions.
    0
    installs
71. ▌
    Field Type Identification · holobiomicslab

    Use when when working with JSON project documents that must conform to a schema-defined structure, and you need to apply type-specific validation, sanitization, or transformation rules (e.g., URL whitespace detection, numeric range checking, mandatory field enforcement).
    0
    installs
72. ▌
    JSON Structured Reporting · holobiomicslab

    Use when you need to persist and communicate the health status of multiple external web services queried during an annotation run.
    0
    installs
73. ▌
    Model Metadata Validation · holobiomicslab

    Use when after deploying a TensorFlow Serving container (especially within a Dockerized stack like NP-Classifier), before running classification or inference pipelines, to confirm that input layers are named 'input_2048' and 'input_4096' and output layer is named 'output'.
    0
    installs
74. ▌
    Motif Metadata Annotation · holobiomicslab

    Use when after LDA inference has produced a trained motifset (motifset.json or motifset_optimized.json) with Mass2Motif probability distributions over fragments and neutral losses.
    0
    installs
75. ▌
    Mzpeak File Io Operations · holobiomicslab

    Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability across languages and tools; (2) load mzPeak spectrum or chromatogram data into memory as structured tables for analysis;
    0
    installs
76. ▌
    Openapi Schema Generation · holobiomicslab

    Use when when you have a webservice codebase (Python, Java, etc.) with HTTP route definitions, parameter handling, and serialization logic, and you need to generate an OpenAPI 3.
    0
    installs
77. ▌
    Organism Taxonomy Mapping · holobiomicslab

    Use when you have a cleaned organism table (with validated, deduplicated organism names from sources like NCBI, manual curation, or previous cleaning steps) and need to annotate each organism with Open Tree of Life identifiers, taxonomic lineage, and standardized taxonomic annotations.
    0
    installs
78. ▌
    Otl Identifier Assignment · holobiomicslab

    Use when after organism name cleaning and taxonomy verification (4_cleaningTaxonomy.R) have been completed and you have a cleaned organism table with standardized names.
    0
    installs
79. ▌
    Pathway Database Querying · holobiomicslab

    Use when when preparing to run ORA on a metabolomics study: you have a list of detected metabolites from your experiment and need to determine which metabolites from the full pathway database should serve as the statistical background, and which pathways contain how many metabolites overall.
    0
    installs
80. ▌
    Release Branch Management · holobiomicslab

    Use when you need to validate that a software project's release branch is stable and ready for distribution. Specifically, use it when: (1) a release tag has been created or code pushed to a release branch; (2) you need to confirm that CI/CD pipelines execute without failures;
    0
    installs
81. ▌
    Repository Administration · holobiomicslab

    Use when you need to validate that a scientific software project's continuous integration pipeline is functional and producing reproducible builds—particularly before releasing new versions, after merging changes to release branches, or when troubleshooting build failures that block distribution of.
    0
    installs
82. ▌
    Spectrum Array Validation · holobiomicslab

    Use when after applying any sequence of spectrum preprocessing operations (set_mz_range, remove_precursor_peak, filter_intensity, scale_intensity) to an MsmsSpectrum object, to confirm that the resulting arrays fall within specified m/z windows, intensity bounds, and peak count limits before.
    0
    installs
83. ▌
    Anndata Object Annotation · holobiomicslab

    Use when after loading or merging spatial metabolomics data into an AnnData object (via read_sm_csv_as_anndata, read_sm_imzml_as_anndata, or merge_sm_pos_neg), and before filtering or normalization steps.
    0
    installs
84. ▌
    Batch Name Reconciliation · holobiomicslab

    Use when when you have a metadata table with taxonomic annotations (species, genus, family columns) that may contain outdated, misspelled, or non-canonical taxon names, and you need to integrate these samples into a natural products analysis pipeline that requires standardized taxonomy (e.
    0
    installs
85. ▌
    Build Artifact Validation · holobiomicslab

    Use when after completing a platform-specific build (e.g., mvn clean package, qmake6 && make, cmake && make) to confirm the generated artifact is not corrupted and can execute on the intended OS (Windows 10, Ubuntu 22.04, macOS 12+ ARM64, or other documented targets).
    0
    installs
86. ▌
    Classifier Output Parsing · holobiomicslab

    Use when after a classifier (such as BitterPredict.m) has computed binary predictions (e.g., bitter vs. non-bitter) on a batch of molecular descriptors and you need to organize those predictions into a structured, labeled output file for downstream analysis, validation, or reporting.
    0
    installs
87. ▌
    Command Sequence Ordering · holobiomicslab

    Use when you have a workflow.csv file co-located with sequence.csv in a session directory, and you need to initialize a reproducible, ordered chain of processing steps (e.
    0
    installs
88. ▌
    Compound Query Formatting · holobiomicslab

    Use when you have a set of chemical compounds (identified by name, SMILES, InChI, or other standard identifier) that you need to classify using ClassyFire, and you must prepare them as a single batch query body for the submit_query POST request.
    0
    installs
89. ▌
    Data Structure Validation · holobiomicslab

    Use when after converting or filtering objects (e.g., transformation products to suspect lists, feature groups through componentization) and before passing them to downstream functions like screenSuspects or generateComponents.
    0
    installs
90. ▌
    Database Record Retrieval · holobiomicslab

    Use when you need to access a stored chemical structure, NRP sequence, or building-block annotation from the MassSpecBlocks database in order to export it to an external format (e.g., CycloBranch), transform it for mass spectra analysis, or integrate it with another chemical database query.
    0
    installs
91. ▌
    Diagnostic Plot Rendering · holobiomicslab

    Use when when you have computed statistical or classification results (e.
    0
    installs
92. ▌
    Dimple Pipeline Execution · holobiomicslab

    Use when when you have deposited mass spectrometry imaging data in NetCDF (CDF) format paired with MATLAB workspace files (.
    0
    installs
93. ▌
    Eic Signal Peak Detection · holobiomicslab

    Use when after EIC candidate generation from LC/HRMS data (mzXML, mzML, or netCDF formats), when you need to localize discrete peaks within chromatographic profiles and assign retention time boundaries, apex intensities, and quality scores prior to peak annotation or cross-sample alignment.
    0
    installs
94. ▌
    Field Exclusion Filtering · holobiomicslab

    Use when when transforming tabular data via the matrix directive and you need to copy most or all fields from input records into output dictionaries, but must explicitly exclude certain named fields (e.
    0
    installs
95. ▌
    Graph Centrality Analysis · holobiomicslab

    Use when after constructing a network (adjacency matrix, edge list, or correlation network) when you need to identify which nodes are most central to network topology.
    0
    installs
96. ▌
    Graph Community Detection · holobiomicslab

    Use when you have a sparse inverse covariance graph (GLASSO output) and multivariate PCA scores for the same samples/variables, and you need to partition the network into functionally or statistically coherent sub-networks rather than treating the graph as a monolithic structure.
    0
    installs
97. ▌
    Image Intensity Jittering · holobiomicslab

    Use when when preparing ion images (single-channel 2D arrays or multi-channel spectral images) from mass spectrometry imaging for contrastive learning in DeepION's COL or ISO modes.
    0
    installs
98. ▌
    Indexed Gzip File Parsing · holobiomicslab

    Use when you have compressed mzML.gz files and need to retrieve specific spectra by numeric identifier without decompressing the entire file.
    0
    installs
99. ▌
    Isotope Pattern Detection · holobiomicslab

    Use when you have MS1-format mass spectrometry files and need to determine the isotope count for peptide features without manual inspection or expert parameter tuning.
    0
    installs
100. ▌
     Jvm Dependency Resolution · holobiomicslab

     Use when when you have obtained source code for a Maven-based Java project and need to determine whether your local build environment can successfully compile it, or when preparing to reproduce a published CI/CD build workflow from a GitHub Actions or similar pipeline configuration.
     0
     installs