← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

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

1. ▌
   Validation Error Categorization · holobiomicslab

   Use when when a parsed mwTab file (MS or NMR experimental data) must be assessed for conformance to its corresponding JSON schema specification. Apply this skill after loading the mwTab file using the mwtab parser but before quality assurance sign-off or deposition to the Metabolomics Workbench.
   6 installs
2. ▌
   Webassembly Local Loading Setup · holobiomicslab

   Use when you have downloaded a web application (e.g., COLMARvista) that uses WebWorker and WebAssembly components and need to run it locally by opening index.html in a browser, rather than accessing it through a web server.
   6 installs
3. ▌
   Atac Seq Tn5 Bias Correction · holobiomicslab

   Use when you have raw ATAC-seq BAM files and need to perform footprinting analysis to detect transcription factor binding through Tn5 insertion patterns.
   4 installs
4. ▌
   Hi C Map Artifact Validation · holobiomicslab

   Use when after executing the Juicer pipeline on raw Hi-C FASTQ files, to confirm that the pipeline has generated the expected .hic output artifact and that the contact matrix construction and normalization steps completed without error.
   3 installs
5. ▌
   Batch Document Verification · holobiomicslab

   Use when when you have deposited a collection of JSON project documents in a platform and need to verify that all conform to the published schema before public release or after schema updates.
   4 installs
6. ▌
   Batch Prediction Comparison · holobiomicslab

   Use when when you have a trained molecular classifier (like BitterPredict) that accepts structured descriptor input, and you need to understand which chemical descriptor subgroups drive prediction outcomes.
   5 installs
7. ▌
   Chemical Identifier Mapping · holobiomicslab

   Use when you have .msp spectral library files with compound names but lack standardized chemical identifiers (SMILES, InChI, InChI Key, CAS number, IUPAC names, or molecular formulas).
   7 installs
8. ▌
   Embedding Vector Validation · holobiomicslab

   Use when after instantiating and invoking a sinusoidal formula embedding layer (such as SCARF embeddings in MIST-CF) on chemical formula inputs, validate that the output embeddings meet dimensionality and value constraints before using them for downstream transformer or ranking tasks.
   7 installs
9. ▌
   Error Handling Confirmation · holobiomicslab

   Use when when implementing or auditing a data replacement method (e.g., `mz<-`, `intensity<-`) in an MsBackend subclass that must enforce ordering or format constraints on peak data.
   7 installs
10. ▌
    Figure Table Interpretation · holobiomicslab

    Use when you need to verify claims about algorithm performance, data processing correctness, or workflow outcomes in a scientific article or software repository. Use it when source documents contain figures, tables, or visualization badges (e.
    5 installs
11. ▌
    Git Repository Tag Checkout · holobiomicslab

    Use when when you need to reproduce or validate a specific historical release artifact (e.g., a Semantic Release v1.0.
    5 installs
12. ▌
    Graph Serialization Graphml · holobiomicslab

    Use when after constructing a network graph where nodes represent Mass2Motifs (or spectra) and edges encode pairwise spectral similarity scores, and you need to export the network for visualization, post-processing, or sharing with collaborators using standard graph software (e.
    6 installs
13. ▌
    Im Ms Drift Time Correction · holobiomicslab

    Use when when you have IM-MS lipidomics data acquired on samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and need to quantify systematic CCS bias and apply lipid class-specific bias correction to all measured CCS values, particularly when multiple lipids per lipid.
    5 installs
14. ▌
    Metadata Field Verification · holobiomicslab

    Use when you have located a workflow definition file (YAML or JSON) from a versioned release and need to confirm that all mandatory workflow metadata fields (name, version, inputs, outputs, steps) are declared, properly formatted, and cross-references are resolved before validation or execution.
    7 installs
15. ▌
    Package Integration Testing · holobiomicslab

    Use when you need to verify that a Python package (or similar installable software) passes its declared integration test suite as a prerequisite to trusting its reliability in production or downstream analysis. Specifically, apply it when you observe a periodic testing CI workflow badge (e.
    3 installs
16. ▌
    Pathway Coverage Assessment · holobiomicslab

    Use when when preparing to run Over-representation Analysis (ORA) on a metabolomics study, after constructing the background set but before running the enrichment test.
    6 installs
17. ▌
    Pytest Test Suite Execution · holobiomicslab

    Use when after installing a package in development mode (e.g., via `pip install -e .[dev]`) to verify the package functions as intended, or before submitting pull requests to confirm no regressions were introduced by code changes.
    3 installs
18. ▌
    Python Source Code Analysis · holobiomicslab

    Use when you have a Python webservice codebase (e.g., a Flask, Django, or FastAPI application) and need to document its HTTP API surface (endpoints, methods, parameters, schemas, authentication) for integration, testing, or specification generation.
    8 installs
19. ▌
    Reference Library Alignment · holobiomicslab

    Use when when you have IM-MS lipidomics data with measured CCS values from samples spiked with U13C labeled internal standards, and you need to assess systematic CCS bias or enable CCS correction by comparing measured lipids against known library entries with validated CCS values.
    7 installs
20. ▌
    Release Artifact Generation · holobiomicslab

    Use when when a software project has reached a stable milestone (v-tagged commit) and you need to produce official distribution artifacts with verified version metadata, checksums, and release documentation that can be validated against a published GitHub release record.
    4 installs
21. ▌
    Repository History Analysis · holobiomicslab

    Use when when you need to understand how a complex feature or architectural pattern was implemented in a codebase, particularly when the current README or documentation does not fully explain the control flow, decision criteria, or parameter passing between subsystems.
    5 installs
22. ▌
    Rust Build System Execution · holobiomicslab

    Use when you have obtained a Rust source repository (e.g., mzpeak_prototyping) and need to compile it into a working command-line converter tool or library. Use this skill when the source includes a Cargo.
    6 installs
23. ▌
    Scientific Task Formulation · holobiomicslab

    Use when you are starting a new mass spectrometry analysis task or feature request where the problem scope is unclear, the tool chain (e.g., OpenMS + Python + KNIME integration) is not yet selected, or acceptance criteria (code quality, test coverage, documentation) have not been established.
    4 installs
24. ▌
    Software Plugin Development · holobiomicslab

    Use when when you have a scientific software tool (e.g., Met-ID) that is architected to support plugins or configuration-driven modules, and you need to register and apply a novel reagent, derivatizing matrix, or analytical method (e.
    6 installs
25. ▌
    Sparsity Metric Computation · holobiomicslab

    Use when when you have loaded a dataset of molecular fingerprint vectors (such as biosynfoni fingerprints from a Zenodo deposit) and need to quantify how sparse the bit-representations are—that is, what fraction of bit positions are zero across the fingerprint collection.
    7 installs
26. ▌
    Tima Entry Point Validation · holobiomicslab

    Use when when you have obtained or are considering use of the tima Docker image (adafede/tima-r) and need to confirm that the containerized environment is operational before proceeding with metabolite annotation workflows. This is a smoke test to catch environment or registry issues early.
    4 installs
27. ▌
    Twim Ms Calibration Mapping · holobiomicslab

    Use when you have raw or processed arrival-time data from a TWIM-MS instrument and need to convert it to CCS values for comparison across experiments or biomolecular classes.
    4 installs
28. ▌
    Abstract Syntax Tree Design · holobiomicslab

    Use when when you have a domain-specific query language (such as MassQL for mass spectrometry) and need to convert query strings into structured representations that preserve domain constraints (e.g., mass tolerance, scan type, intensity thresholds).
    6 installs
29. ▌
    Abundance Matrix Processing · holobiomicslab

    Use when you have multiple CSV files containing feature-by-sample matrices from different analytical experiments or batches, each with mass, retention time, intensity, isotope, and adduct information across different samples.
    6 installs
30. ▌
    Adduct Ion Mass Calculation · holobiomicslab

    Use when when you have derivatized metabolite structures (SMILES or mol format) and need to predict their ionization products in MS imaging, particularly when the derivatizing matrix produces non-standard adducts (e.
    5 installs
31. ▌
    Anova Pvalue Adjustment Fdr · holobiomicslab

    Use when you have completed ANOVA or G-test statistical testing across multiple biomolecules in an omics dataset and need to account for multiple testing.
    5 installs
32. ▌
    API Response Error Handling · holobiomicslab

    Use when when building asynchronous metadata enrichment workflows that call multiple external APIs (CIR, CTS, PubChem, IDSM, BridgeDb) to annotate mass spectra .
    4 installs
33. ▌
    Byte Offset Seek Operations · holobiomicslab

    Use when when you have an indexed gzip-compressed mzML file and need to retrieve individual spectra or chromatograms by index without sequential file reading or full decompression. Typical scenario: you want spectrum[42] from a 10 GB indexed mzML.gz file and need sub-second access time.
    4 installs
34. ▌
    C Python Interface Wrapping · holobiomicslab

    Use when you have a mature C++ library (like OpenMS) with stable APIs that you want to make accessible from Python environments, and you need to preserve performance-critical C++ execution while supporting rapid prototyping or integration into Python-based data pipelines (e.
    5 installs
35. ▌
    Candidate Structure Ranking · holobiomicslab

    Use when you have (1) a set of candidate structures generated by in silico fragmentation (e.g., MetFrag output), (2) one or more seed nodes with known spectral library matches or identity scores, and (3) a fragmentation relationship graph connecting candidates.
    7 installs
36. ▌
    Ccs Prediction Model Design · holobiomicslab

    Use when you have a dataset of molecules with known or reference CCS values, and you need to construct a trainable model that learns the mapping from molecular structure (encoded as SMILES or feature vectors) to scalar CCS predictions.
    6 installs
37. ▌
    Circular Barplot Generation · holobiomicslab

    Use when after running a comprehensive preprocessing workflow comparison (e.g., via normulticlassqcall or nortimecoursenoall) that produces an overall ranking CSV file of candidate workflows.
    7 installs
38. ▌
    Contrastive Pair Generation · holobiomicslab

    Use when you have raw ion images from MSI data and need to train a contrastive encoder to learn stable, mode-specific representations.
    5 installs
39. ▌
    Covariance Matrix Inversion · holobiomicslab

    Use when after generating a covariance matrix from normalized metabolite abundance data in MetaboAnalyst, and before performing network-level metabolomic inference or visualizing metabolite interaction networks.
    7 installs
40. ▌
    Data Integrity Verification · holobiomicslab

    Use when after applying matchms metadata cleaning tools to normalize field values and standardize naming conventions on imported spectra (mzML, mzXML, msp, MGF, or JSON formats).
    6 installs
41. ▌
    Dictionary List Aggregation · holobiomicslab

    Use when after applying a matrix directive variant (fields_to_headers, headers, or collate) to extract and transform individual records into dictionaries with field filtering and type coercion applied.
    6 installs
42. ▌
    Distance Geometry Embedding · holobiomicslab

    Use when when you have ionized adduct structures (in SMILES or MOL format) from an upstream ionization-state determination step and need to produce multiple low-energy 3D conformations for collision cross section prediction, metabolite annotation, or structure-property modeling.
    6 installs
43. ▌
    Distance Metric Computation · holobiomicslab

    Use when after obtaining CNN-predicted embeddings for query mass spectra and having loaded pre-computed embeddings from a reference database, you need to identify which reference molecules are most similar to each query.
    6 installs
44. ▌
    Dna Adduct Characterization · holobiomicslab

    Use when when you have a collection of DNA adduct compound structures in SDF format that requires validation for structural integrity and completeness, and you need to generate predicted fragment spectra at defined ionization levels and mass ranges for comparison against experimental mass.
    5 installs
45. ▌
    Docker Container Deployment · holobiomicslab

    Use when you need to launch a pre-built Docker image of a scientific tool (e.
    4 installs
46. ▌
    Domain Composition Analysis · holobiomicslab

    Use when you have a set of Biosynthetic Gene Clusters in GenBank format and need to understand the domain architecture of constituent genes, either to detect statistically significant domain co-occurrence patterns within BGCs, to filter redundant BGCs by domain similarity, or to link detected.
    6 installs
47. ▌
    Embedding Vector Generation · holobiomicslab

    Use when when you have tokenized mass spectra (peak-mass and peak-intensity pairs from experimental or in-silico libraries such as NIST 2017 or MassBank) and need to perform rapid similarity searches or spectrum matching at scale.
    5 installs
48. ▌
    Entry Status Classification · holobiomicslab

    Use when you need to assess the overall curation coverage and quality of a MIBiG repository snapshot, identify which entries require further review, or track how entry validation status changes over time. Specifically use it when the `data` directory contains JSON files with `cluster.
    6 installs
49. ▌
    File Format Standardization · holobiomicslab

    Use when when you have raw outputs from LipidSearch or LIQUID identification software (CSV or TSV format with vendor-specific column naming and lipid identifiers) and need to construct a structured data matrix suitable for batch normalization, statistical testing, or visualization.
    4 installs
50. ▌
    Filter Parameter Validation · holobiomicslab

    Use when reconstructing or modifying dashboard filters (e.
    5 installs
51. ▌
    Format Conversion Chemistry · holobiomicslab

    Use when when you have retrieved a user database entry (sequence or structure data) from the MassSpecBlocks backend and need to enable mass spectra analysis in the open-source CycloBranch program, or when you need to export NRP sequences and building-block annotations for consumption by external.
    5 installs
52. ▌
    Ftms Transient Data Loading · holobiomicslab

    Use when you have a Bruker Solarix FT-ICR transient file in .d format (e.g., ESI_NEG_SRFA.d containing ser and fid files in CompassXtract format) and need to programmatically load it into a Python environment for signal processing, calibration, and mass spectrum generation.
    8 installs
53. ▌
    Ggplot2 Pie Chart Rendering · holobiomicslab

    Use when you have a frequency table (generated by count_fold_changes and converted to relative abundance via ra_table) of metabolite subsets stratified by class or direction of change (e.g., increased vs. decreased organic acids at padj ≤ 0.
    6 installs
54. ▌
    Group Comparison Statistics · holobiomicslab

    Use when after data integration, batch correction, and sample separation when you have a feature-by-sample abundance matrix (finalData) and corresponding sample group labels (finalLabel), and your research goal is to identify which metabolites significantly differ between experimental groups for.
    5 installs
55. ▌
    Hpc Job Array Orchestration · holobiomicslab

    Use when you have a machine learning training workflow (e.g., k-fold cross-validation) where each fold is independent, GPU-accelerated, and can run in parallel.
    7 installs
56. ▌
    Imms Data Format Conversion · holobiomicslab

    Use when when you have raw Agilent MassHunter (.d) or UIMF IM-MS data files from drift tube (DT) or structure for lossless ion manipulations (SLIM) instruments and need to ingest them into a preprocessing pipeline that requires standardized in-memory or intermediate representations for.
    7 installs
57. ▌
    Interactive Plot Generation · holobiomicslab

    Use when you have loaded m/z and intensity arrays from an MZA file (via mzapy) and need to inspect a mass spectrum, extracted ion chromatogram (XIC), or arrival time distribution (ATD) visually, either for QC purposes, method development, or publication-ready output.
    2 installs
58. ▌
    Ionization State Prediction · holobiomicslab

    Use when when you have SMILES strings representing neutral organic molecules and need to enumerate the likely protonated (e.g., [M+H]+) and deprotonated (e.
    6 installs
59. ▌
    Kaleido Backend Integration · holobiomicslab

    Use when when a Shiny application currently uses orca for static plot export but requires a lighter-weight, Python-native alternative that avoids Node.js/Electron runtime overhead.
    9 installs
60. ▌
    Local Maxima Identification · holobiomicslab

    Use when you have raw LC-HRMS profile-mode data and need to identify candidate chromatographic peaks before classification or feature extraction.
    3 installs
61. ▌
    Maplet Function Composition · holobiomicslab

    Use when you have metabolomics data that requires sequential processing through multiple analytical steps (e.
    3 installs
62. ▌
    Metabolic Model Gap Filling · holobiomicslab

    Use when you have consensus metabolic reconstructions in SBML or JSON format for community members and need to resolve incomplete reactions, missing cofactor availability, or blocked pathways that prevent feasibility of biomass production.
    5 installs
63. ▌
    Metabolite Id Normalization · holobiomicslab

    Use when you have metabolite identifiers sourced from or annotated against heterogeneous metabolome databases (HMDB, ChEBI, PubChem, KEGG, LipidMaps) and need to resolve ambiguity in metabolite identity, create a unified metabolite reference table, or enable cross-database queries in a metabolomics.
    6 installs
64. ▌
    Metadata Structure Checking · holobiomicslab

    Use when after loading a metadata file but before merging it with positive and negative mode m/z peaklists. Apply this skill when you have a candidate metadata table (e.
    5 installs
65. ▌
    Model Layer Name Validation · holobiomicslab

    Use when when deploying a TensorFlow Serving instance for the NP Classifier or any model-agnostic service where client code hardcodes layer names; before running inference pipelines; after model updates or configuration changes to catch layer name drift early.
    4 installs
66. ▌
    Molecular Format Conversion · holobiomicslab

    Use when when ingesting raw chemical structure data from multiple external sources (publications, databases, contributor submissions) that use different molecular file formats (SMILES strings, SDF files, or other representations), and you need to unify them into a single canonical format before.
    3 installs
67. ▌
    Multi Format Data Ingestion · holobiomicslab

    Use when you have raw metabolomics data files in one or more of the supported formats (.raw from Thermo instruments, .d directories from Agilent, or mzXML open-format exports) and need to ingest them into SMART for preprocessing, visualization, or statistical analysis.
    4 installs
68. ▌
    Multi Omic Data Integration · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z dimensions, and you need to assign biomolecular class labels and compute class-specific CCS values across multiple compound classes simultaneously, particularly when you lack pre-identified feature peaks or want to bypass.
    6 installs
69. ▌
    Multiomics Data Integration · holobiomicslab

    Use when when you have matched multiomics measurements across the same samples or cell lines (transcriptomics, proteomics, metabolomics, epigenomics, etc.) and need to train predictive models that learn regulatory relationships across biomolecular classes.
    3 installs
70. ▌
    Multiple Testing Correction · holobiomicslab

    Use when whenever you have performed Fisher's exact test or another statistical enrichment test on multiple pathways, lipid categories, or metabolite sets simultaneously (typically ≥2 tests, often 50–100+ tests in practice).
    6 installs
71. ▌
    Mzml Mzxml Spectrum Reading · holobiomicslab

    Use when when you have raw mzML or mzXML files containing uncompressed m/z and intensity arrays and need to load spectra into a uniform data contract before compression, cross-format comparison, or algorithmic processing.
    4 installs
72. ▌
    Mzpeak Format Io Operations · holobiomicslab

    Use when you have mass spectrometry run data (spectra, chromatograms, instrument metadata) that must be stored in or recovered from the mzPeak format, or when you need to validate that a mzPeak implementation correctly supports both read and write paths for round-trip fidelity.
    6 installs
73. ▌
    Nested JSON Path Resolution · holobiomicslab

    Use when when applying str directives during JSON-to-JSON conversion and the source value is not a direct field but is nested within a table structure—specifically when you need to reference a specific record by record_id, or traverse a sequence of field names (table → fields → nested value) to.
    8 installs
74. ▌
    Network Graph Serialization · holobiomicslab

    Use when you have applied graphical lasso (GLASSO) to estimate a sparse inverse covariance matrix from a feature matrix and need to convert the non-zero precision matrix entries into an explicit graph representation suitable for visualization, topology analysis, or overlay with PCA scores.
    5 installs
75. ▌
    Nuget Dependency Resolution · holobiomicslab

    Use when you are preparing to build a .NET project (WPF, class library, or console application) and need to ensure all declared NuGet package dependencies are available in the build environment. This is particularly necessary when the project uses custom or private package sources (e.
    5 installs
76. ▌
    Openms API Surface Exposure · holobiomicslab

    Use when when you need to make OpenMS C++ classes, functions, or data structures callable from Python code, or when verifying that a newly bound C++ component can be imported and instantiated without errors in a Python environment.
    5 installs
77. ▌
    Pandas Accessor Integration · holobiomicslab

    Use when you have mass-spectrometry data in a Pandas DataFrame and need to expose plot kinds (spectrum, chromatogram, mobilogram, peakmap) as a `.plot(kind='...
    4 installs
78. ▌
    Postgresql Record Insertion · holobiomicslab

    Use when after successful gensim LDA inference has produced a JSON result file (e.g., myexp.ldaresult.json) and you need to make those topic assignments and model parameters queryable and accessible to a Django web application.
    5 installs
79. ▌
    Ppm Mass Accuracy Filtering · holobiomicslab

    Use when when processing imzML/ibd Imaging Mass Spectrometry datasets and you need to extract ion density maps for specific analytes or isotopes. Apply this skill after importing the .imzML metadata and .
    5 installs
80. ▌
    Python Object Serialization · holobiomicslab

    Use when after constructing a peak properties dictionary via csv_to_peak_properties or other data transformation steps, and before passing the dictionary to subsequent SMITER simulation functions (fragmentor selection, noise injection, mzML generation).
    5 installs
81. ▌
    Pytorch Graph Serialization · holobiomicslab

    Use when you have constructed molecular graphs with atom features (atomic number, degree, formal charge, hybridization) and bond features (bond type, aromaticity) from SMILES or MOL files using RDKit, and need to feed them into a PyTorch-based GNN training pipeline without memory overhead or I/O.
    4 installs
82. ▌
    Pytorch Inference Execution · holobiomicslab

    Use when you have a pretrained PyTorch model with released weights (e.g., JESTR on NPLIB1), a prepared dataset with input features (spectra m/z–intensity arrays, molecular graphs), a GPU environment with CUDA 11.
    4 installs
83. ▌
    Pytorch Tensor Manipulation · holobiomicslab

    Use when when you have parsed molecular graph representations (atom nodes, bond edges, feature vectors) from SMILES or molecular structure files and need to prepare them for forward passes through a pre-trained GNN encoder in PyTorch.
    5 installs
84. ▌
    Qt Widget Rendering Control · holobiomicslab

    Use when you need to restrict a Qt widget's display to a subset of its managed items—such as filtering isotope species in a metabolomics visualization—where the active subset is defined by application preferences stored outside the widget itself.
    6 installs
85. ▌
    R Data Frame Transformation · holobiomicslab

    Use when when you have autoQ output containing peak area measurements for isotopologues in data frame format and need to prepare data for metBarPlot visualization or cross-sample comparison. Specifically, use this skill when val.to.
    6 installs
86. ▌
    R Data Object Serialization · holobiomicslab

    Use when you have mzPeak files (Parquet-based archives containing mass spectrometry spectra and chromatogram data) that you want to analyze in R, and you need to convert the Arrow columnar representation into native R objects that can be passed to downstream analysis functions (e.
    5 installs
87. ▌
    R List Object Serialization · holobiomicslab

    Use when after extracting structured metadata (e.g., instrument parameters, scan counts, time ranges) from Thermo Fisher Scientific .
    6 installs
88. ▌
    R Package Version Detection · holobiomicslab

    Use when before launching the DaDIA metabolomics pipeline or any analysis that requires specific R package versions. Apply this skill when you have access to an R environment and need to verify that R ≥4.0, XCMS ≥3.11.4, and metaMS ≥1.25.1 are installed and compatible.
    7 installs
89. ▌
    Ranked Gene List Generation · holobiomicslab

    Use when you have identified significant differential metabolites (DAMs) from metabolomic profiling, mapped them to genes via enrichment (e.g., MSEA), and possess a gene/protein interaction network (e.g., STRING).
    8 installs
90. ▌
    Repository File Enumeration · holobiomicslab

    Use when you need to inventory sequence files in a repository's designated directory and cross-reference them against public databases to identify sequences that are unique to the curated archive.
    5 installs
91. ▌
    REST API Client Integration · holobiomicslab

    Use when you have a batch of chemical compounds (identifiers and structures in SMILES, InChI, or IUPAC format) that need to be submitted to a remote REST API for classification or analysis, and you require the server's response (query ID and status) to track or retrieve results asynchronously.
    15 installs
92. ▌
    Runtime Comparison Analysis · holobiomicslab

    Use when when a new version or variant of a tool claims performance improvements over a prior version (e.g., MASST+ vs. MASST), and you need empirical evidence that the claimed speedup (e.g., ~100-fold reduction in search time) is real, reproducible, and quantifiable.
    9 installs
93. ▌
    Schema Conformance Checking · holobiomicslab

    Use when you have a collection of records in a standardized format (e.g., MassBank plain-text or structured records) that must be validated before commit or publication.
    4 installs
94. ▌
    Semantic Metabolite Ranking · holobiomicslab

    Use when you have an unknown metabolite with unknown mass spectrum and need to prioritize structural candidates from databases (PubChem, HMDB) by their likelihood of being the true compound.
    6 installs
95. ▌
    Sequence To Feature Mapping · holobiomicslab

    Use when when you have a list of polypeptide sequences (plain text, CSV, or FASTA format) and need to compute their monoisotopic mass and average mass for downstream mass spectrometry interpretation, database matching, or physico-chemical property annotation.
    5 installs
96. ▌
    Shifted Dot Product Scoring · holobiomicslab

    Use when matching query mass spectra to a spectral library in the presence of unknown post-translational modifications (PTMs) or non-enzymatic modifications.
    7 installs
97. ▌
    Shiny Interface Development · holobiomicslab

    Use when you have a complete R package (e.g., pmartR) implementing a multi-step omics analysis pipeline (upload → transform → filter → normalize → test → visualize), and you want to make those steps accessible to scientists who lack R expertise.
    5 installs
98. ▌
    Software Regression Testing · holobiomicslab

    Use when after implementing code changes to MS2Query (e.g., modifying the workflow branching logic for true library matches vs. analog search results), before committing or pushing to the repository.
    4 installs
99. ▌
    Spectral Data Preprocessing · holobiomicslab

    Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct-injection MS (DI-MS), ASAP-MS, or other ambient ionization instruments (AI-MS, LDI-MS), and you need to identify peaks of interest, assign confidence scores, and prepare the data for database matching or species.
    7 installs
100. ▌
     Spectral Peak Normalization · holobiomicslab

     Use when when preparing query spectra and library spectra for similarity-based matching via dot product scoring, particularly in open modification spectral library searches where you need to match modified query spectra to unmodified library counterparts without the results being biased by.
     5 installs