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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Peak M Z Indexing · holobiomicslab

   Use when when you have LC-MS-MS metabolomics data in MGF format and need to prepare it for unsupervised analysis (e.g., topic modeling with LDA).
   13 installs
2. ▌
   Mnar Data Handling · holobiomicslab

   Use when you have metabolomics data (targeted LC/MS or untargeted GC/MS) with left-censored missing values below the limit of quantification (LOQ) or limit of detection (LOD), and you need to impute these values while preserving the underlying distributional structure and avoiding bias from.
   12 installs
3. ▌
   Msp To CSV Parsing · holobiomicslab

   Use when you have a .msp format MS/MS spectrum library (e.g., from MassBank or similar public databases) and need to convert it into individual CSV entries indexed by positive or negative ionisation mode for use as a custom fragment library in MetaboAnnotatoR annotation pipelines.
   12 installs
4. ▌
   Mzml Mzxml Parsing · holobiomicslab

   Use when you have raw LC-MS/MS data in mzML or mzXML format and need to isolate specific MS1/MS2 scan pairs for a targeted compound list or for building a local spectral library.
   9 installs
5. ▌
   Peak Count Capping · holobiomicslab

   Use when apply peak-count capping when preprocessing tandem mass spectrometry (MS/MS) spectra for peptide identification or spectral library matching, particularly when working with high-resolution spectra that may retain numerous low-intensity noise peaks after intensity filtering.
   12 installs
6. ▌
   Topic Modeling Lda · holobiomicslab

   Use when after generating a corpus/features JSON file from raw MS2 fragmentation spectra or similar document-term data, when the goal is unsupervised discovery of latent topics (e.g., metabolite families or spectral motifs) without ground-truth labels.
   11 installs
7. ▌
   Usi String Parsing · holobiomicslab

   Use when when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/Yao_Streptomyces/roseosporus/0518_s_BuOH.
   10 installs
8. ▌
   Evidence Linking · holobiomicslab

   Use when you have tandem MS/MS spectra annotated by at least two of GNPS (FBMN), ISDB-LOTUS (CFM-ID 4.0 spectral matching), and Sirius 6, and you need to rank features by annotation agreement rather than trust a single tool's output.
   11 installs
9. ▌
   Output Grounding · holobiomicslab

   Use when when developing or extending mass spectrometry data processing workflows (e.
   8 installs
10. ▌
    Gcf Table Export · holobiomicslab

    Use when you have completed a BiG-SLiCE v2 clustering run and need to extract the pre-calculated BGC and GCF cluster assignments in TSV format for postprocessing, integration with SQL pipelines, or sharing with collaborators who require flat tabular output rather than the SQLite database or.
    10 installs
11. ▌
    Asb Metabolomics · holobiomicslab

    Use when starting any task with the ASB Metabolomics skill collection — read this meta-skill first. It explains good practice (search -> apply -> ground), enforces the license-tier acknowledgment for non-open tools, then hands off to the _router skill for actual skill selection.
    13 installs
12. ▌
    Bgc Mf Link Scoring · holobiomicslab

    Use when you have preprocessed GCF-MF link pairs from paired genomics–metabolomics datasets (antiSMASH-detected BGCs clustered into GCFs, and GNPS spectra grouped into MFs) and need to rank them by likelihood of representing true natural product–biosynthetic gene associations.
    12 installs
13. ▌
    File I O Automation · holobiomicslab

    Use when you have MZmine-exported LC-MS/MS data (MGF spectra and CSV metadata files) in both positive and negative ionization modes and need to execute the full MolNotator pipeline from duplicate filtering through dereplication and network generation.
    13 installs
14. ▌
    Gcf Mf Link Scoring · holobiomicslab

    Use when after BGC detection and clustering (producing GCFs) and metabolomics profiling (producing MFs with MS/MS spectra), when you have paired genomic and metabolomic data from the same microbial strains and need to rank which GCF–MF pairs are likely to represent true biosynthetic relationships.
    10 installs
15. ▌
    Pyteomics API Usage · holobiomicslab

    Use when when you have polypeptide sequences and need to compute their monoisotopic or average mass, isotopic distribution patterns, or other physico-chemical properties; or when you need to parse and manipulate MS/LC-MS data, FASTA databases, or search engine output in a Python workflow.
    11 installs
16. ▌
    R Package API Usage · holobiomicslab

    Use when when you have metabolomics data (tab-delimited text or SummarizedExperiment object) and need to apply batch correction, outlier detection, internal standard recommendation, and quality filtering at scale or in non-interactive workflows.
    11 installs
17. ▌
    Tabular Data Export · holobiomicslab

    Use when you have extracted MS1 or MS2 peak lists and scan headers from Thermo Fisher RAW files using MetaXtract and need to load them into pandas, NumPy, or external analysis tools.
    13 installs
18. ▌
    Peak Table Extraction · holobiomicslab

    Use when you have raw or converted spectral data (jcamp, RAW, or mzML format) from NMR, IR, or MS instruments and need to identify individual peaks, extract their properties (chemical shift, m/z, intensity, width), and generate a structured peak table for annotation, comparison, or publication.
    11 installs
19. ▌
    Tabular Data Cleaning · holobiomicslab

    Use when you have a CSV or table-format spectral peak list (with chemical shift, intensity, and metadata columns) destined for NMRformer or similar peak-to-metabolite assignment models, and you need to exclude low-quality peaks that would otherwise harm prediction accuracy.
    10 installs
20. ▌
    JSON File Parsing · holobiomicslab

    Use when when you have JSON-formatted curation data organized in a directory structure (e.g., the MIBiG `data` directory) and need to extract a specific nested field (e.g., `cluster.status`) across all entries to build an index, summary table, or quality report.
    12 installs
21. ▌
    Kegg API Querying · holobiomicslab

    Use when after metabolite KEGG identifiers and hierarchy metadata have been assigned (via assign_hierarchy with 'KEGG' identifier) and you need to enrich your metabolomics count data frame with functional orthology and associated gene information from KEGG.
    11 installs
22. ▌
    2d Tic Preprocessing · holobiomicslab

    Use when when you have raw GCxGC-MS data imported from NetCDF into a 2D-TIC chromatogram object and need to remove chemical and instrumental noise (column bleeding, baseline drift, detector contamination) to reveal metabolite differences between sample groups for downstream multiway PCA or.
    8 installs
23. ▌
    Drift Time Filtering · holobiomicslab

    Use when you have loaded a raw GCIMS dataset and need to isolate the region of interest in drift time (typically 5–16 ms for small organic molecules) to exclude low-drift-time chemical noise, high-drift-time tail artifacts, or off-scale ion signals that would degrade subsequent alignment and peak.
    11 installs
24. ▌
    Lcms Raw Data Import · holobiomicslab

    Use when you have raw LC/MS data in mzML or mzXML format and need to initiate untargeted metabolomics analysis.
    12 installs
25. ▌
    Ms Scan File Parsing · holobiomicslab

    Use when you have acquired a Thermo mass spectrometry RAW file (or other proprietary instrument format) and need to extract MS1 and/or MS2 scans in an open, interoperable format (mzML, MGF, or Raxport-processed FT1/FT2 files) for TIC visualization, PSM scoring, or stable isotope labeling analysis.
    9 installs
26. ▌
    Ms2lda Motif Mapping · holobiomicslab

    Use when you have a GNPS-generated molecular network (either classical or feature-based) and corresponding MS2LDA experiment output containing Mass2Motif-to-spectrum assignments, and you want to visualize which substructural motifs are shared across clusters or features and how they distribute.
    9 installs
27. ▌
    Peak List Formatting · holobiomicslab

    Use when after successfully resolving a USI string to a specific mass spectrum scan, and before performing spectral matching, library search, or comparative analysis.
    5 installs
28. ▌
    Sample Label Mapping · holobiomicslab

    Use when you have a raw peak table (CSV format, from any of 12 supported LC-MS software tools or standardized format) and a separate label file that assigns each sample to an experimental class (e.
    7 installs
29. ▌
    Xcms Profile Parsing · holobiomicslab

    Use when you have xcms-processed LC-MS data with detected feature groups (from xcms grouping), suspect retention time misalignment across samples due to long acquisition periods or large sample cohorts, and need to feed raw profiles into ncGTW's realignment algorithm.
    8 installs
30. ▌
    JSON Schema Validation · holobiomicslab

    Use when you have loaded an mwTab file into a structured MWTabFile object and need to verify it conforms to MS or NMR schema specifications before deposition, curation, or downstream analysis.
    10 installs
31. ▌
    Nmr Peak Deconvolution · holobiomicslab

    Use when when you have raw or processed 1D NMR spectra (FID or frequency-domain format) and need to extract individual peak identities and quantitative parameters in tabular form.
    13 installs
32. ▌
    API Data Retrieval · holobiomicslab

    Use when you need to obtain all project JSON documents currently deposited in a data platform (such as the Paired Omics Data Platform) to validate their structure against a JSON Schema specification, or when you require a complete snapshot of published records for quality assurance, data migration.
    13 installs
33. ▌
    Bgc Cluster Export · holobiomicslab

    Use when you have completed a BiG-SLiCE v2 clustering analysis and need to convert the internal SQLite3 database results into human-readable, tabular TSV files for import into spreadsheet applications, statistical tools, or custom analysis pipelines that do not support SQLite3 directly.
    12 installs
34. ▌
    Data Deduplication · holobiomicslab

    Use when after parsing and validating a .csv file containing comma-separated SMILES strings, and before formatting the molecule list for CypReact input.
    10 installs
35. ▌
    Jndi Binding Setup · holobiomicslab

    Use when deploying a Java web application (such as CEU Mass Mediator) that requires access to an internal or external database and the application server provides JNDI as the connection pooling and naming mechanism.
    7 installs
36. ▌
    R Function Calling · holobiomicslab

    Use when after AutoTuner has completed peak identification (TIC analysis), peak isolation, and EIC parameter extraction on at least 3 raw mass spectrometry samples (qTOF, orbitrap, or FTICR formats converted to mzML/mzXML/CDF), and you need to export the tuned parameters in a format ready for XCMS.
    13 installs
37. ▌
    R Script Execution · holobiomicslab

    Use when you have located example R scripts in a version-controlled repository (e.g., Codes-Explained folder), a Read-Me.txt file documents the purpose and parameters of each script, and you need to reconstruct or validate a simulation procedure for a specific data sub-sample scenario.
    11 installs
38. ▌
    S3 Method Dispatch · holobiomicslab

    Use when your metabolomics data frame has inherited or assigned class metadata (e.
    10 installs
39. ▌
    Smiles Sdf Parsing · holobiomicslab

    Use when you have a natural product molecule or compound library provided as SMILES strings, InChI strings, or SDF files, and you need to convert them into an in-memory molecular representation (RDKit Mol object) suitable for fingerprinting, property prediction, or other cheminformatic operations.
    8 installs
40. ▌
    Ms Data Preprocessing · holobiomicslab

    Use when you have received raw CE-MS or LC-MS output files in vendor-specific formats from a mass spectrometry instrument and need to process them through an untargeted metabolomics workflow (e.g., AriumMS) that requires standardized, interoperable file formats.
    11 installs
41. ▌
    Xic Marker Annotation · holobiomicslab

    Use when when you have a resolved spectrum file (mzML, mzXML) and need to visualize where MS2 precursor scans occur on an XIC display.
    8 installs
42. ▌
    Mzml File Import Xcms · holobiomicslab

    Use when you have raw mzML files from a mass spectrometry instrument and need to begin a preprocessing workflow in xcms. This is the essential first step before any peak detection (centWave, MSWParam) or feature grouping can occur.
    9 installs
43. ▌
    Fragment Ion Matching · holobiomicslab

    Use when you have two tandem mass spectra (query and reference) with precursor m/z and fragment ion peaks, and you need to identify which fragment ions correspond between them to assess spectral similarity, detect structural variants, or validate compound identifications.
    12 installs
44. ▌
    Hmdb Formula Sampling · holobiomicslab

    Use when when you need to create in silico LC-MS/MS experiments with diverse chemical backgrounds for testing fragmentation strategies or acquisition controllers, and you want the chemical diversity to reflect real metabolomic samples. Use this when you have a target m/z range (e.
    8 installs
45. ▌
    Mass Defect Filtering · holobiomicslab

    Use when after MS-Dial peak picking and feature table construction, when you observe a high proportion of features with anomalous m/z decimal values that are inconsistent with known metabolite ionization patterns.
    12 installs
46. ▌
    Mass Track Clustering · holobiomicslab

    Use when after constructing initial data bins from mzTree (indexed by int(mz × 1000)), determine whether a single bin contains one or multiple mass tracks. Apply clustering when the m/z range of points in a bin exceeds 2 × ppm tolerance (e.
    8 installs
47. ▌
    Motif To Node Mapping · holobiomicslab

    Use when you have a GNPS-generated classical or feature-based mass spectral molecular network (graphml or JSON format) and a corresponding MS2LDA experiment with Mass2Motif assignments on the same spectra, and you want to visualize and quantify which structural motifs are shared within and across.
    12 installs
48. ▌
    Mz Decimal Extraction · holobiomicslab

    Use when after loading a feature table with m/z values from MS-Dial output when you need to identify and remove features with anomalous decimal m/z values.
    9 installs
49. ▌
    Mzml Spectral Parsing · holobiomicslab

    Use when when beginning a metabolomics annotation workflow with raw MS2 spectral data in .mzML format. This step is necessary when you have vendor-converted or standard .
    10 installs
50. ▌
    Newick Format Parsing · holobiomicslab

    Use when you have a Chemical Feature Tree artifact (phylogeny) output from q2-qemistree's make-hierarchy method and need to verify its structural validity, count nodes (leaves and internal nodes), measure tree depth, and assess branching patterns before using it for alpha- or beta-diversity.
    11 installs
51. ▌
    Peak Shape Assessment · holobiomicslab

    Use when after peak detection in a nontargeted LC-MS workflow when you have a feature table with detected peaks and need to filter low-quality features or understand why certain features have inconsistent intensity or poor annotation confidence.
    13 installs
52. ▌
    Slack API Integration · holobiomicslab

    Use when rapid QC-MS detects a QC failure (e.g., internal standard retention time drift, m/z deviation, or intensity anomaly) during an active LC-MS instrument run and users have configured Slack as a notification target.
    9 installs
53. ▌
    Spectral JSON Parsing · holobiomicslab

    Use when after submitting an LC-MS/MS fragmentation spectrum to the MSNovelist web service and receiving a JSON response containing ranked de-novo structure candidates.
    14 installs
54. ▌
    Spectrum Data Loading · holobiomicslab

    Use when when you have a USI (e.g., mzspec:MTBLS1124:QC07.mzML) pointing to a public mzML or related spectrum file in MetaboLights, MassIVE, or GNPS repositories, and need to load the spectrum data for interactive visualization, quality control assessment, or downstream analysis.
    11 installs
55. ▌
    Upset Plot Generation · holobiomicslab

    Use when after loading and filtering search results from two or more DIA-MS analysis tools at a specified Q-value cutoff, when you need to summarize which analytes are identified by all tools, by specific subsets, or uniquely by individual tools.
    13 installs
56. ▌
    Usi Namespace Parsing · holobiomicslab

    Use when when you need to retrieve mass spectrometry spectrum data from a metabolomics repository but only have a USI string (e.g., 'mzspec:GNPS:TASK-c95481f0c53d42e78a61bf899e9f9adb-spectra/specs_ms.mgf:scan:1943' or 'mzspec:MASSBANK::accession:SM858102').
    13 installs
57. ▌
    Entrypoint Verification · holobiomicslab

    Use when when you have obtained a Python package from a repository (e.g., via git clone) and need to confirm that the documented Python version constraint and pinned dependency versions are sufficient to execute the package's main entry point (typically main.py or a console script).
    9 installs
58. ▌
    Nmr Spectral Processing · holobiomicslab

    Use when you have raw NMR/IR/MS spectral data in vendor-specific (RAW), open (jcamp), or mass spectrometry (mzML) formats and need to parse, validate, and convert them to a standardized internal representation with extracted metadata and peak tables for visualization or further analysis in.
    11 installs
59. ▌
    Bedgraph File Export · holobiomicslab

    Use when after computing per-bin coverage depth using cooltools.coverage() on a loaded cooler object, when you need to (1) share the coverage track with non-Python tools, (2) visualize it in a genome browser, or (3) integrate it with downstream analyses that expect bedGraph or tabular input.
    10 installs
60. ▌
    Data Quality Gating · holobiomicslab

    Use when after curating and integrating structure-organism pairs from heterogeneous sources when you need to enforce quality thresholds before publishing or analyzing a reference dataset.
    8 installs
61. ▌
    Manifest Generation · holobiomicslab

    Use when you maintain a local repository of biological sequences (such as MIBiG) and need to produce a searchable inventory that links local files to their metadata and external database availability status.
    10 installs
62. ▌
    Msi Data Import CSV · holobiomicslab

    Use when you have MSI intensity data exported from MSiReader or SCiLS software as a plain-text CSV file (with peaks as columns and pixels/spots as rows), and you need to import it into R to perform pairwise mass difference calculations and adduct identification.
    10 installs
63. ▌
    Msi Peak Annotation · holobiomicslab

    Use when you have processed MSI data (peak matrix and spatial coordinates) from matrix-assisted laser desorption/ionization (MALDI) or silver-assisted laser desorption/ionization (AgLDI) experiments, and you need to computationally distinguish matrix ions from analyte ions before downstream feature.
    10 installs
64. ▌
    Script File Mapping · holobiomicslab

    Use when you have edited core algorithm scripts in the Core-Match GitHub repository and need to integrate those changes into a locally installed LipidMatch-4.2 distribution (downloaded from innovativeomics.com). The trigger is the presence of modified .
    14 installs
65. ▌
    Sdf File Processing · holobiomicslab

    Use when you have molecular structures (from databases, design tools, or literature) that need to be analyzed for CYP reactivity or metabolic properties, and you must convert them into a format compatible with the CypReact command-line tool.
    6 installs
66. ▌
    Tsv File Generation · holobiomicslab

    Use when after completing a BiG-SLiCE v2 clustering analysis on an input folder of BGCs, when you need to retrieve the computed BGC and GCF cluster membership tables in a portable, widely-compatible tabular format rather than querying the SQLite database directly.
    10 installs
67. ▌
    Wpf Gui Compilation · holobiomicslab

    Use when when you have cloned the MsdialWorkbench repository and need to produce an executable WPF GUI application (MsdialGuiApp) for Windows.
    9 installs
68. ▌
    Metabolomics Workflow Router · holobiomicslab

    Use when a user has a whole metabolomics analysis GOAL (e.g. "annotate my untargeted LC-MS/MS data", "find biomarkers", "where else has this molecule been seen") rather than a single step — select the right end-to-end composite workflow super-skill, then run its stages, grounding each against its source papers.
    8 installs
69. ▌
    Gtf File Parsing · holobiomicslab

    Use when you have a GTF-formatted genome annotation file and need to generate alternative splicing events (exon skipping, intron retention, alternative splice sites, mutually exclusive exons) or transcript-isoform inclusion levels (PSIs).
    13 installs
70. ▌
    Candidate Rank Scoring · holobiomicslab

    Use when after compound database dereplication has generated per-spectrum candidate lists (e.
    10 installs
71. ▌
    Chemical Class Mapping · holobiomicslab

    Use when you have a GNPS molecular network (GML or GraphML format) and wish to annotate network nodes with chemical class labels to support metabolite family interpretation. Use it specifically when you need to overlay chemical classification schemes (e.
    7 installs
72. ▌
    Genome Sequence Mining · holobiomicslab

    Use when you have assembled genomic DNA sequences (contigs in FASTA format, not antiSMASH or BOA output) and corresponding LC-MS/MS data (in MGF, mzXML, mzML, or mzData format) from the same organism, and you want to identify novel RiPPs by linking gene cluster predictions to observed mass spectra.
    14 installs
73. ▌
    JSON Record Enrichment · holobiomicslab

    Use when when a project JSON record contains a resolvable public identifier (genome accession, biosynthetic gene cluster ID, etc.) but lacks the corresponding human-readable or standardized metadata field (organism name, cluster description).
    12 installs
74. ▌
    Lc Ms Data Calibration · holobiomicslab

    Use when when you have paired LC-MS measurements from labeled and unlabeled samples of the same analytes, and you need to isolate the true isotopic labeling contribution by removing confounding signal from naturally occurring isotopes and tracer isotopic impurity.
    12 installs
75. ▌
    Mass Delta Computation · holobiomicslab

    Use when when you have parsed two or more MS/MS spectra (precursor m/z and fragment ion lists) and need to quantify all pairwise mass differences between fragment ions before alignment or similarity scoring.
    8 installs
76. ▌
    Mass Error Calculation · holobiomicslab

    Use when when screening LC-HRMS datasets for suspect compounds: you have detected features with measured m/z values and a database of reference compounds with theoretical m/z values, and you need to rank candidate matches by mass accuracy before proceeding to retention time and fragmentation.
    8 installs
77. ▌
    Ms Dial Output Parsing · holobiomicslab

    Use when you have completed peak picking in MS-DIAL (generating files like Urine_RP_NEG_norm.txt or Urine_RP_POS_norm.txt) and need to load the resulting feature table into R for quality control, feature filtering, normalization, or metabolite annotation.
    11 installs
78. ▌
    Ms Ms Raw Data Loading · holobiomicslab

    Use when when you have raw LC-MS/MS instrument output files (e.g., .mzML, .
    15 installs
79. ▌
    Ms Ms Spectrum Parsing · holobiomicslab

    Use when you have raw or preprocessed MS/MS spectra in one of the supported formats (MGF, mzML, mzXML, JSON, MSP, mzXML, pickled matchms objects, or USI) and need to extract peak lists (m/z and intensity pairs) along with metadata (precursor m/z, charge, ionization mode) to feed into MS2Query or.
    10 installs
80. ▌
    Ms1 Feature Extraction · holobiomicslab

    Use when when you have an LC-HRMS feature table (with m/z values, retention times, and isotopic signatures) and a suspect compound database (with reference m/z, expected retention time windows, isotope ratios, and neutral loss fragments), and you need to rapidly prioritize which features are most.
    14 installs
81. ▌
    Mzml Format Generation · holobiomicslab

    Use when after completing a virtual LC-MS/MS acquisition simulation using ViMMS (e.g., after calling env.
    8 installs
82. ▌
    Mzml Format Validation · holobiomicslab

    Use when after downloading an mzML file from a remote repository (e.g., MetaboLights, MassIVE, GNPS) via USI resolution, before attempting to parse it into a spectrum container or visualization dashboard.
    10 installs
83. ▌
    Peak M Z Recalibration · holobiomicslab

    Use when after peak detection when you have a table of detected peaks with m/z values and need to improve mass accuracy for downstream annotation.
    9 installs
84. ▌
    Spectrum Peak Matching · holobiomicslab

    Use when you have an experimental tandem mass spectrum (peaks with m/z values and intensities), a chemical formula, and a set of candidate molecular structures retrieved from a database like PubChem.
    9 installs
85. ▌
    Subformula Enumeration · holobiomicslab

    Use when when performing chemical noise removal on MS/MS spectra and you need to validate whether each fragment ion m/z is consistent with loss of a subformula from the precursor ion.
    10 installs
86. ▌
    HTTP API Endpoint Design · holobiomicslab

    Use when when you need to expose a multi-step spectral processing workflow (parse → extract → render → annotate → compress) as a web service endpoint that accepts jcamp/RAW/mzML spectral files and must return coordinated output artifacts (modified JCAMP files, peak tables, and PNG images) in a.
    10 installs
87. ▌
    Mwtab To JSON Conversion · holobiomicslab

    Use when you have mwTab-formatted files from the Metabolomics Workbench containing MS or NMR experimental metadata and data blocks that need to be converted to JSON for integration with REST APIs, web applications, or downstream tools that expect JSON input.
    13 installs
88. ▌
    Python Environment Setup · holobiomicslab

    Use when when you have cloned a scientific Python repository (e.g., ROIAL-NMR) and need to verify that the documented dependencies can be installed and the main entrypoint is invokable without errors. Use this skill before attempting to run the application's core analysis workflows.
    7 installs
89. ▌
    Spectral Image Rendering · holobiomicslab

    Use when when you have parsed and validated spectral data (jcamp, RAW, or mzML format) from NMR/IR/MS instruments and need to create visual representations with peak annotations for inspection, annotation, or publication.
    8 installs
90. ▌
    Spectral Peak Validation · holobiomicslab

    Use when before feeding a peak list into the NMRformer model or other transformer-based spectral assignment frameworks.
    12 installs
91. ▌
    Bedpe Format Handling · holobiomicslab

    Use when your ChIP-Seq input is paired-end sequencing data stored in BEDPE format (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.gz), and you need to estimate fragment length and call peaks while respecting the paired nature of the reads rather than treating them as independent single-end alignments.
    11 installs
92. ▌
    R Package Champ Usage · holobiomicslab

    Use when when you have raw methylation array data (450K or EPIC format) in .idat files or as a beta-valued matrix and need to conduct a complete analysis pipeline including data import, quality filtering, normalization, batch effect correction, DMR detection, or gene set enrichment.
    10 installs
93. ▌
    Status Value Parsing · holobiomicslab

    Use when when a project README or documentation embeds badge endpoints that report real-time status (e.g., Travis CI build, Landscape.
    8 installs
94. ▌
    Unit Test Validation · holobiomicslab

    Use when when you need to confirm that a research tool or package maintains a functioning test suite, especially before adopting it for downstream analysis or before contributing modifications. Triggered by the presence of a CI workflow badge (e.
    11 installs
95. ▌
    C Module Integration · holobiomicslab

    Use when you have raw mass spectrometry data in mzML or mzXML format and need to compress it using a format-agnostic compressor that expects a standardized spectral data contract.
    11 installs
96. ▌
    Feature Pair Ranking · holobiomicslab

    Use when you have two feature matrices from different modalities (e.
    11 installs
97. ▌
    M Z Array Processing · holobiomicslab

    Use when when you have imported MSI data (imzML or vendor format) loaded into the napari plugin environment and need to organize raw spectral m/z and intensity arrays prior to mean intensity calculation, ROI analysis, or database annotation.
    8 installs
98. ▌
    Static Code Analysis · holobiomicslab

    Use when when preparing to submit a pull request to a collaborative Python project (like BiG-SCAPE) that mandates PEP8 compliance, or when establishing quality gates for a codebase that has adopted linters as part of its contribution guidelines.
    11 installs
99. ▌
    Wikidata Integration · holobiomicslab

    Use when when building or maintaining a local natural-product reference database that requires current Wikidata entries, or when preparing metadata for mass-spectrometry queries that need enriched compound annotations (e.g., alternative names, chemical classifications, source organisms).
    11 installs
100. ▌
     Ms Ms Spectrum Matching · holobiomicslab

     Use when you have a cleaned and clustered set of LC-MS features (m/z, retention time, MS/MS spectra) from MS-CleanR output and need to assign putative compound identities by matching observed MS/MS fragmentation patterns against reference spectral libraries using HRR-based scoring.
     10 installs