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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Multi Score Complementarity Evaluation · holobiomicslab

   Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine whether they capture complementary information that justifies combining them.
   0 installs
2. ▌
   Multidimensional Signal Smoothing Imms · holobiomicslab

   Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains jagged, low-abundance ion peaks or when saturation repair has been applied and the resulting reconstructed signals need artifact removal and enhancement.
   0 installs
3. ▌
   Mzml File Generation Mass Spectrometry · holobiomicslab

   Use when after frequency-based denoising and sample-level aggregation of replicate MS/MS spectra, when you need to export denoised spectra to a standardized, vendor-independent format compatible with spectral matching pipelines.
   0 installs
4. ▌
   Online Proteomics Resource Integration · holobiomicslab

   Use when your analysis requires MS/MS spectra from public proteomics datasets but you want to avoid manual download and format conversion.
   0 installs
5. ▌
   Pathway Activity Decomposition Via Svd · holobiomicslab

   Use when when you have a metabolite intensity matrix (samples × metabolites) with compound annotations and need to score pathway activity levels for pathway enrichment analysis.
   0 installs
6. ▌
   Pathway Activity Propagation Inference · holobiomicslab

   Use when when you have an untargeted metabolomics feature table (m/z values, retention times, intensity measurements, and p-values from statistical testing) and want to predict which metabolic pathways are active, but metabolite identification is incomplete, unreliable, or computationally expensive.
   0 installs
7. ▌
   Peak Recovery From Filtered Candidates · holobiomicslab

   Use when after applying cluster-based filtering with quasi-molecular adducts and frequency thresholds on candidate metabolites from KEGG matching.
   0 installs
8. ▌
   Peptide Sequence Prediction Comparison · holobiomicslab

   Use when when you have a pre-trained Casanovo model, annotated MS/MS spectra in MGF format, and want to benchmark whether beam search decoding improves peptide prediction quality over the default greedy decoding strategy.
   0 installs
9. ▌
   Qc Metric Visualization Across Samples · holobiomicslab

   Use when you have processed LC-MS peak detection output or feature tables containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to visually monitor whether internal standards are within acceptable QC.
   0 installs
10. ▌
    Retention Time Alignment Index Mapping · holobiomicslab

    Use when when processing multiple LC-MS samples with varying scan numbers or retention-time drift, before constructing composite mass tracks for peak detection.
    0 installs
11. ▌
    Retention Time Calibration Integration · holobiomicslab

    Use when you have LC-MS data from authentic standards run in positive and negative ESI modes, converted to .mzML format, and you need to build an in-house metabolite reference library for untargeted identification workflows.
    0 installs
12. ▌
    Retention Time Drift Time M Z Querying · holobiomicslab

    Use when you have multidimensional MS data converted to MZA HDF5 format and need to retrieve specific spectra or chromatographic slices defined by one or more of: retention time (in minutes), ion mobility arrival time (in milliseconds for DT/SLIM or Vs/cm² for TimsTOF), or m/z value (as a float or.
    0 installs
13. ▌
    Retention Time Mass Proximity Matching · holobiomicslab

    Use when after sample alignment and grouping of isotopologues and adducts have been completed, when the aligned feature table contains NA or zero entries (missing intensities) for features that are detected in some samples but fall below the detection threshold in others.
    0 installs
14. ▌
    Sample Type Stratified Feature Masking · holobiomicslab

    Use when after feature detection but before statistical analysis, when your study includes blank samples (e.g., solvent or extraction blanks) and you want to remove features that fail to show meaningful enrichment in actual study samples relative to blank contamination.
    0 installs
15. ▌
    Small Molecule Chromatography Modeling · holobiomicslab

    Use when when you have a set of small molecule structures (as SMILES or molecular graphs) and need to predict their elution order in RPLC systems with eluent pH around 2.
    0 installs
16. ▌
    Snakemake Dag Generation And Execution · holobiomicslab

    Use when you have multiple mzML or mzML.gz files from LC-IMS-MS/MS instruments and need to apply DEIMoS feature detection, alignment, and calibration operations in a reproducible, traceable manner.
    0 installs
17. ▌
    Spectra Annotation Parsing And Pairing · holobiomicslab

    Use when when loading MS/MS spectra from MGF files for FIDDLE model training or evaluation, or when preparing spectrum–annotation pairs for rescore model data augmentation (TCN train/test sets).
    0 installs
18. ▌
    Spectra Variable And Peak Data Storage · holobiomicslab

    Use when when building a new mass spectrometry data backend for the Spectra package that must store and serve multiple spectra with their associated m/z and intensity peaks. Use this when you need a backend that combines efficient metadata lookup (via data.
    0 installs
19. ▌
    Spectral Consensus Spectrum Generation · holobiomicslab

    Use when after extracting and filtering top-TIC spectra for a given feature (e.
    0 installs
20. ▌
    Spectral Database Output Normalization · holobiomicslab

    Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON objects, TSV match tables) that need to be reconciled into a single normalized schema for downstream aggregation.
    0 installs
21. ▌
    Spectral Fingerprint Web Service Query · holobiomicslab

    Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural classification (compound class and subclass) with confidence estimates.
    0 installs
22. ▌
    Spectral Format Parsing And Validation · holobiomicslab

    Use when you have raw or unprocessed MS/MS spectral data in standard metabolomics formats (MGF, mzML, mzXML, msp, or JSON) and need to import them into a Python-based workflow for MS2 fingerprint generation, peak counting, or spectral similarity scoring.
    0 installs
23. ▌
    Spectral Library Export And Formatting · holobiomicslab

    Use when after theoretical spectra have been generated for lipid–adduct combinations with enumerated fragment masses and intensities, and you need to deploy them for downstream MS/MS analysis on Orbitrap (DDA via Excalibur) or SkyLine (targeted/PRM) workflows.
    0 installs
24. ▌
    Spectral Molecular Embedding Alignment · holobiomicslab

    Use when you have MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures for an unknown compound spectrum by learning a joint embedding space rather than using traditional spectral similarity or.
    0 installs
25. ▌
    Spectral Noise Filtering Preprocessing · holobiomicslab

    Use when you have raw MS/MS spectral data and plan to calculate spectral similarity scores (whether using entropy distance, dot product, or other algorithms) for compound identification.
    0 installs
26. ▌
    Spectral Peak Intensity Interpretation · holobiomicslab

    Use when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict which fragments will appear with high intensity in a tandem MS spectrum, or when you are performing structural elucidation by ranking candidate molecules against experimental spectra and need.
    0 installs
27. ▌
    Spectral Similarity Matrix Computation · holobiomicslab

    Use when after preprocessing and filtering mass spectra (peak filtering, metadata cleaning) when you need to compare all spectrum pairs within a dataset or between a query set and a reference library to identify similar or related spectra.
    0 installs
28. ▌
    Spectral Similarity Network Generation · holobiomicslab

    Use when after feature detection and alignment across LC-MS/MS runs (via MZmine2 or Optimus) have produced a feature quantification table and MGF file with MS/MS spectra, and you need to discover molecular relationships and detect unknown compounds through spectral clustering and library matching.
    0 installs
29. ▌
    Structure Prediction From Mass Spectra · holobiomicslab

    Use when you have GNPS-style MGF spectral files from MS/MS experiments and need to predict the molecular structure (as SMILES) of unknown compounds.
    0 installs
30. ▌
    Tandem Ms Data Annotation And Curation · holobiomicslab

    Use when you have an unknown tandem MS/MS spectrum (precursor m/z and fragment peaks) and need to infer the molecular formula and ionization mode (e.g., [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+) in a de novo setting without access to spectral libraries.
    0 installs
31. ▌
    Tandem Ms Spectral Data Interpretation · holobiomicslab

    Use when you have untargeted MS2 spectral data in MS2MP-compatible format and need to assign KEGG pathway annotations to spectra without spectral library matching or manual compound identification.
    0 installs
32. ▌
    Time Resolved Dbdi Data Interpretation · holobiomicslab

    Use when you have time-resolved DBDI-MS data (intensity matrix with m/z features as rows and scan timepoints as columns) from direct injection analysis where chromatographic separation is unavailable and you need to identify which features represent fragments or adducts of the same parent compound.
    0 installs
33. ▌
    Transformation Product Data Extraction · holobiomicslab

    Use when after generating or obtaining a TP object (via generateTPs with library, in-silico, or BioTransformer algorithms) that contains SMILES, InChIKey, or formula information for transformation products, and you need to screen those TPs in LC-HRMS data or annotate them using MetFrag.
    0 installs
34. ▌
    Validated Link Proportional Comparison · holobiomicslab

    Use when when you have scored GCF-MF (gene cluster family–molecular family) links using two or more complementary scoring approaches (e.g., standardised strain correlation and IOKR), and you need to determine whether combining scores improves discrimination of true links from false positives.
    0 installs
35. ▌
    Vendor Format Recognition And Handling · holobiomicslab

    Use when when Rapid QC-MS receives vendor-format LC-MS acquisition files from instrument data folders and must prepare them for automated QC checks and MS-DIAL processing. Specifically: input files are in proprietary vendor formats (Thermo .raw, Bruker .d, Sciex .
    0 installs
36. ▌
    Workflow Pipeline Execution Validation · holobiomicslab

    Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically informed annotation pipeline, or after pipeline execution to verify all outputs were generated correctly.
    0 installs
37. ▌
    Xcms Object Handling And Preprocessing · holobiomicslab

    Use when you have raw gas or liquid chromatography–mass spectrometry data (in NetCDF or mzML format) and need to detect features, align them across samples by retention time and mass-to-charge ratio, correct for retention time drift, and fill missing values before downstream metabolite clustering.
    0 installs
38. ▌
    Xcms Ramclustr Data Object Integration · holobiomicslab

    Use when when you have raw LC-MS all-ion fragmentation (AIF) chromatograms in centroid mode and need to prepare them for metabolite annotation using fragment ion matching.
    0 installs
39. ▌
    Chemical Database Querying And Retrieval · holobiomicslab

    Use when you have BioTransformer-predicted metabolite structures (in SMILES or InChI format) and need to identify which known compounds in public databases match those structures.
    0 installs
40. ▌
    Fragmentation Pattern Similarity Scoring · holobiomicslab

    Use when after feature detection and alignment have produced a feature table with MS/MS spectra, and you have access to a reference spectral database (e.g., xenobiotic reaction libraries or public databases).
    0 installs
41. ▌
    Metabolomics Data Loading And Formatting · holobiomicslab

    Use when you have raw metabolomics count data (e.g., from mass spectrometry or NMR experiments) in tabular format and associated sample metadata (e.g., treatment groups, experimental factors) that need to be imported into R for analysis with packages like Omu.
    0 installs
42. ▌
    Microbiome Metabolome Data Preprocessing · holobiomicslab

    Use when when starting with raw paired microbiome (16S rRNA, metagenomic taxonomic or functional features) and metabolome (LC-MS/MS, NMR) count tables from the same biospecimens, and planning to train prediction models or co-abundance networks.
    0 installs
43. ▌
    Molecular Graph Encoder Decoder Training · holobiomicslab

    Use when when you have a training dataset of NMR spectra-derived molecular fragments encoded as token sequences, and you need to predict both the molecular formula and complete bond connectivity of unknown molecules.
    0 installs
44. ▌
    Molecular Structure Conformer Generation · holobiomicslab

    Use when you have 2D molecular structures (SMILES or SDF format) and need to create 3D conformer geometries as input to subsequent computational chemistry workflows, such as CCS prediction, molecular graph construction, or voxel-based property calculations.
    0 installs
45. ▌
    Multiple Testing Correction Metabolomics · holobiomicslab

    Use when you have computed raw p-values from partial Spearman correlations (or other univariate tests) between each metabolite in a SummarizedExperiment object and a phenotype of interest, adjusted for epidemiological confounders (e.
    0 installs
46. ▌
    Nmr Spectrum Reconstruction From Library · holobiomicslab

    Use when you have an NMR spectrum of a mixture sample and a library of reference spectra for individual compounds.
    0 installs
47. ▌
    Per Browser Developer Setting Navigation · holobiomicslab

    Use when you are attempting to run a web application (such as COLMARvista) locally by opening index.html directly in a browser, the application uses WebWorker and/or WebAssembly components, and these fail to load due to default file-access policies.
    0 installs
48. ▌
    Spectral To Structure Mapping Prediction · holobiomicslab

    Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra from an unknown organic compound with ≤19 heavy atoms, and you need to recover its molecular structure (both formula and connectivity) rapidly without access to 2D NMR experiments (HSQC, HMBC, COSY) or mass spectrometry.
    0 installs
49. ▌
    Bias Corrected Z Score Interpretation · holobiomicslab

    Use when after computeDeviations has generated a SummarizedExperiment object with z-score assays reflecting bias-corrected deviations of observed vs. expected accessibility at motif or kmer sites.
    0 installs
50. ▌
    Clustering Accuracy Metric Extraction · holobiomicslab

    Use when when you need to reproduce or validate benchmark comparisons between clustering methods on single-cell chromatin accessibility data, particularly when the source publication reports multiple accuracy metrics across heterogeneous datasets and you must decide which method variant (e.
    0 installs
51. ▌
    Compressed Sparse Row Matrix Handling · holobiomicslab

    Use when you have a raw or preprocessed single-cell count matrix (from BAM-to-fragment or FASTQ-to-matrix pipelines) and need to apply matrix-free algorithms like tl.spectral, tl.multi_spectral, or other scalable dimension reduction methods that require dense or sparse matrix input.
    0 installs
52. ▌
    Contact Frequency Smoothing Log Space · holobiomicslab

    Use when you have a precomputed expected contact frequency table (TSV with columns: dist_bp, contact_frequency, n_valid) derived from cooler Hi-C matrices and need to generate a smoothed, log-binned P(s) curve for downstream analysis such as TAD detection, contact probability visualization, or.
    0 installs
53. ▌
    Dna Methylation Differential Analysis · holobiomicslab

    Use when you have merged methylation call data across multiple biological replicates (samples per group ≥2) with base-pair-level coverage information, and you need to identify loci where methylation levels differ significantly between treatment groups.
    0 installs
54. ▌
    Genomic Region Annotation Integration · holobiomicslab

    Use when after bias-correcting ATAC-seq cutsite signal (via ATACorrect) when you have a bias-corrected bigWig file and need to compute per-position footprint scores within defined accessible regions (peaks, called footprints, or regulatory regions) to detect and quantify transcription factor.
    0 installs
55. ▌
    Kilobase Resolution Genomics Analysis · holobiomicslab

    Use when you have raw Hi-C FASTQ data and need to generate contact maps at kilobase resolution, or you have pre-generated .hic files and need to annotate structural features (loops, domains) for downstream 3D genome analysis.
    0 installs
56. ▌
    Methylation Hyper Hypo Classification · holobiomicslab

    Use when after calculating differential methylation across samples using calculateDiffMeth(), when you need to separately enumerate and extract hyper-methylated (increased methylation) versus hypo-methylated (decreased methylation) bases that meet both statistical significance (q-value < 0.
    0 installs
57. ▌
    Methylkit Database Mode Configuration · holobiomicslab

    Use when when analyzing DNA methylation data from bisulfite sequencing (RRBS, target-capture, or whole-genome) and the dataset is too large to fit comfortably in memory, or when you need to process multiple large samples sequentially without reloading data.
    0 installs
58. ▌
    Motif Annotation Correlation Analysis · holobiomicslab

    Use when you have a chromVARDeviations object with multiple annotation sets (such as JASPAR motifs and kmers) and need to determine which annotation pairs are redundant (high correlation) versus synergistic (high synergy z-scores).
    0 installs
59. ▌
    Overdispersion Correction Application · holobiomicslab

    Use when analyzing differential methylation from bisulfite sequencing data where you suspect overdispersion (variance exceeds binomial expectations), or when comparing uncorrected and corrected statistical tests to determine whether more stringent thresholds are justified by the data.
    0 installs
60. ▌
    Shell Environment Variable Resolution · holobiomicslab

    Use when use this skill during pipeline installation or initialization when you need to locate required external binaries (e.g., bowtie2, samtools, R, Python) but the user has not explicitly provided their installation paths in a configuration file.
    0 installs
61. ▌
    Shell Script Executability Validation · holobiomicslab

    Use when you have cloned a bioinformatics repository (e.g., FredHutch/SEACR) and need to confirm that its shell and R scripts are executable and will run successfully on your input data (e.g., CUT&RUN bedGraph files) before investing time in a full analysis.
    0 installs
62. ▌
    Single Cell Epigenomics Peak Analysis · holobiomicslab

    Use when you have preprocessed single-cell ATAC-seq fragment files or count matrices and need to identify open chromatin regions (peaks) to support downstream differential accessibility analysis, motif discovery, or regulatory network inference.
    0 installs
63. ▌
    Tabix Index Validation And Inspection · holobiomicslab

    Use when after creating a methylRawListDB object via methRead() with dbtype='tabix', or when loading pre-existing tabix-backed methylation files, to verify that bgzipped files are correctly indexed and contain required methylKit metadata headers (≥v1.13.
    0 installs
64. ▌
    Trajectory Inference Method Selection · holobiomicslab

    Use when when you have an ArchR project object with processed single-cell ATAC-seq data and want to infer developmental or cell-state trajectories.
    0 installs
65. ▌
    Activity Score Robustness Assessment · holobiomicslab

    Use when after computing PLAGE-derived activity scores for pathways or metabolite sets (Molecular Families, Mass2Motifs) from log2-standardized metabolomics intensity data.
    0 installs
66. ▌
    Asynchronous Converter Instantiation · holobiomicslab

    Use when building a metadata enrichment system that must support multiple pluggable converter backends and you need to automatically discover all available converters at runtime, extract their conversion specifications, and generate Job tuples that can be dispatched to an async annotation engine.
    0 installs
67. ▌
    Atom Bond Feature Importance Ranking · holobiomicslab

    Use when you have a trained GNN model for molecular property prediction (such as CCS) and need to understand which atomic and bond features are most influential in driving predictions.
    0 installs
68. ▌
    Batch Effect Variance Quantification · holobiomicslab

    Use when after running pycombat batch correction on multi-batch metabolomics feature tables when you need to validate that batch correction has successfully attenuated inter-batch intensity variance without altering the structural integrity (sample and feature counts) of the corrected table.
    0 installs
69. ▌
    Bayesian Meta Learning Model Fitting · holobiomicslab

    Use when you have a pre-trained DNN RT predictor (e.g., trained on METLIN SMRT with 80,038 experimental RTs) and need to adapt it to predict retention times in a new or external chromatographic method for which you have only 10–50 calibration molecules with known RTs.
    0 installs
70. ▌
    Categorical Grouping And Aggregation · holobiomicslab

    Use when you have a flat table of structure-organism pairs or entity records and need to summarize their distribution across categorical bins (e.g., organism counts binned by number of associated structures in categories: 1, 1–10, 10–100, >100).
    0 installs
71. ▌
    Computational Throughput Measurement · holobiomicslab

    Use when when you need to compare the computational efficiency of different mass spectrometry libraries on identical data and processing pipelines, or when you want to establish baseline throughput for a library version and validate claims of performance improvement.
    0 installs
72. ▌
    Container Orchestration Verification · holobiomicslab

    Use when when a software tool is distributed as a Docker image and you need to confirm it is available on a registry (e.g., Docker Hub), that the image pulls without corruption, and that the application's entry point (help command, version output, or interactive shell) is accessible and responsive.
    0 installs
73. ▌
    Corrected Intensity Table Validation · holobiomicslab

    Use when after applying one or more intensity drift correction strategies (Internal Standard correction, statistical drift correction, custom or weighted bracketing) within QuantyFey and before exporting the corrected intensity table for final quantification.
    0 installs
74. ▌
    Data Marshalling And Type Conversion · holobiomicslab

    Use when you have Spectra::Spectra objects in R and need to apply Python MS algorithms from matchms or spectrum_utils (e.g., CosineGreedy similarity scoring, normalization, or filtering), or conversely need to convert Python spectral objects back to R for downstream Spectra workflows.
    0 installs
75. ▌
    Diversity Visualization By Treatment · holobiomicslab

    Use when you have normalized peak-abundance matrices with sample metadata containing categorical treatment variables (e.
    0 installs
76. ▌
    Docker Compose Service Orchestration · holobiomicslab

    Use when when a research software project is decomposed into distinct subproject components (e.
    0 installs
77. ▌
    Docker Container Health Verification · holobiomicslab

    Use when when you have deployed NP Classifier using Docker Compose and need to confirm that both the server and TensorFlow Serving containers are running and healthy before sending SMILES strings to the /classify endpoint.
    0 installs
78. ▌
    Graph Neural Network Model Inference · holobiomicslab

    Use when you have a trained GNN model (stored as .h5 weights) and molecular graph representations (SMILES strings and/or 3D coordinates), and you need to compute predicted CCS values or perform feature importance analysis via ablation or gradient-based saliency mapping.
    0 installs
79. ▌
    Ion Mobility Arrival Time Conversion · holobiomicslab

    Use when you have a feature table containing raw ion mobility arrival time measurements paired with experimentally assigned biomolecular class labels (e.g., lipid, protein, carbohydrate), and you need to compute CCS values for downstream structural or comparative analysis.
    0 installs
80. ▌
    Isotopologue Mass Offset Calculation · holobiomicslab

    Use when you have a peak-picked feature table (HDF5 format with m/z, drift_time, retention_time, intensity columns) and need to identify and label isotopic signatures within singly charged species.
    0 installs
81. ▌
    Mass Difference Pairwise Calculation · holobiomicslab

    Use when after importing MSI data as an msimat object and having a list of detected peak masses, but before annotating which mass differences correspond to biologically plausible adducts.
    0 installs
82. ▌
    Mass Error Calculation And Reporting · holobiomicslab

    Use when after molecular formula assignment has been performed on calibrated m/z values. Apply this skill when you need to quantify the accuracy of formula-to-peak matching, validate mass calibration performance against reference standards (e.g., SRFA.
    0 installs
83. ▌
    Mass Spectrometry Peak Pair Analysis · holobiomicslab

    Use when you have preprocessed MSI data (as a CSV intensity matrix or Cardinal MSProcessedImagingExperiment object) and suspect that observed peaks include both parent ions and their adducts formed with matrix or salt species.
    0 installs
84. ▌
    Mass Spectrometry Polarity Filtering · holobiomicslab

    Use when when processing centroided .mzML LC–MS runs with a multi-polarity target list (i.e., some targets ionize in positive mode, others in negative mode, or both) and you need to detect peaks and extract ion chromatograms without manually subsetting the raw data by polarity beforehand.
    0 installs
85. ▌
    Mass Spectrum Calibration Validation · holobiomicslab

    Use when after applying frequency domain calibration (Ledford, linear, or quadratic equation) to a raw FT-ICR mass spectrum, validate the calibration quality by measuring residual mass errors across the m/z range.
    0 installs
86. ▌
    Metabolite Identification Validation · holobiomicslab

    Use when you have extended a metabolite identification tool (such as Met-ID) to support a new derivatizing matrix beyond the default (e.
    0 installs
87. ▌
    Metabolomics Data Structure Handling · holobiomicslab

    Use when when beginning an LC-MS/MS metabolomics analysis pipeline and you have preprocessed xcms result objects (XcmsExperiment or legacy xcmsSet) that need to be loaded into memory, validated for integrity, and prepared for feature grouping (e.
    0 installs
88. ▌
    Metadata Extraction From Source Code · holobiomicslab

    Use when you need to reverse-engineer or document the architecture of a multi-component research software system where design information is embedded in repository structure, README declarations, setup files, or module docstrings rather than in a separate design document.
    0 installs
89. ▌
    Metadata Transformation Verification · holobiomicslab

    Use when you have extracted raw tabular metadata into JSON form using the MESSES extract command and need to confirm the extraction is accurate before conversion to a repository-specific format. Specifically, use it when the conversion target format has strict schema requirements (e.
    0 installs
90. ▌
    Neural Network Hyperparameter Tuning · holobiomicslab

    Use when when training a neural network to predict metabolite abundances from microbiome data (or similar paired multivariate omics prediction tasks) and you need to avoid overfitting while maximizing predictive accuracy on held-out test data.
    0 installs
91. ▌
    Organism Count Distribution Analysis · holobiomicslab

    Use when you have a flat file of structure-organism pairs (e.
    0 installs
92. ▌
    Percentile Threshold Based Filtering · holobiomicslab

    Use when you have paired genomic-metabolomic link scores (e.
    0 installs
93. ▌
    Polymorphic Class Dispatch In Python · holobiomicslab

    Use when when you have multiple file format variants (compressed indexed gzip, standard gzip, SQLite database, uncompressed mzML) that all need to be read via a unified interface, and you want to avoid a long chain of conditional logic in client code.
    0 installs
94. ▌
    Proforma Notation Parsing Validation · holobiomicslab

    Use when you have peptide sequences with chemical modifications encoded in ProForma notation (e.g., '[Phospho]-PEPTIDE[Carbamidomethyl]-C') and need to validate their syntax, extract modification positions, or prepare them for downstream physico-chemical property calculations (mass, charge, pI).
    0 installs
95. ▌
    Pymzml Spectrum Object Instantiation · holobiomicslab

    Use when when you have mzML spectrum XML already parsed (either from a file, a database query, or an in-memory representation) and need to construct Spectrum or Chromatogram objects that expose methods like accessing MS level, retention time, m/z and intensity arrays, and other metadata.
    0 installs
96. ▌
    R Package Installation And Execution · holobiomicslab

    Use when when you have a new or updated R package available via a non-CRAN repository (such as r-universe) and need to verify it installs cleanly, passes R-CMD-check compliance, and is ready for downstream workflow execution.
    0 installs
97. ▌
    Repository Structure Standardization · holobiomicslab

    Use when a scientific Python package is being moved to a new GitHub organization with different structural conventions (e.g., from a personal lab account to a community-led organization like metabolomics-cloud or scverse).
    0 installs
98. ▌
    Software Support Matrix Construction · holobiomicslab

    Use when you need to determine the full scope of hardware and methodological compatibility for a bioinformatics tool before designing an analytical workflow.
    0 installs
99. ▌
    Spectral Features Module Integration · holobiomicslab

    Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than scalar molecular properties.
    0 installs
100. ▌
     String Concatenation With Delimiters · holobiomicslab

     Use when when you need to aggregate values from multiple records in a JSON input document into a single concatenated string field (e.
     0 installs