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HolobiomicsLab

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1. ▌
   Ion Clustering By Retention Time And Mass · holobiomicslab

   Use when your peak table contains suspected mispicked ions—ions with similar m/z and retention time that likely represent the same metabolite split across multiple features due to preprocessing errors.
   2 installs
2. ▌
   Knowledge Graph Generation And Validation · holobiomicslab

   Use when after completing all per-sample annotation steps (molecular networking, ISDB/spectral matching, SIRIUS/CSI:FingerID, and compounds metadata enhancement with Wikidata IDs and NPClassifier ontology).
   0 installs
3. ▌
   Lcms Feature Detection And Quantification · holobiomicslab

   Use when you have raw LC-MS data (mzML or equivalent format) from a metabolomics experiment and need to extract a reproducible, quantified feature table with intensity measurements before conducting metabolite identification or statistical analysis.
   0 installs
4. ▌
   M Z Database Matching With Mass Tolerance · holobiomicslab

   Use when you have a set of observed m/z values extracted from a Cardinal MSImagingExperiment object, raw LC-MS data, or similar high-throughput MS dataset, and you need to assign them to known metabolites in a reference database (HMDB, Lipidmaps, etc.) with control over mass accuracy tolerance and.
   0 installs
5. ▌
   M Z Retention Time Correspondence Mapping · holobiomicslab

   Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (as metabData objects) acquired under different conditions or at different times, and you need to determine which features in dataset X correspond to which features in dataset Y so their sample.
   0 installs
6. ▌
   Mass Fragment Neutral Loss Representation · holobiomicslab

   Use when when you have raw or minimally processed MS/MS spectra (in positive or negative ion mode) and aim to infer recurring fragmentation patterns (Mass2Motifs) using topic modeling.
   0 installs
7. ▌
   Mass Spec Tolerance Parameter Application · holobiomicslab

   Use when when you have a feature table from Orbitrap LC-MS containing m/z, retention time, and intensity columns, and you need to group individual mass features into putative metabolites that represent the same chemical entity across different ionization states and isotopic compositions.
   0 installs
8. ▌
   Mass Spectrometer Simulator Configuration · holobiomicslab

   Use when when you have a list of chemical compounds (with m/z values, retention times, and intensities) and need to simulate their acquisition behavior under a specific ionization polarity and mass spectrometer configuration.
   0 installs
9. ▌
   Mass Spectrometry Chromatogram Extraction · holobiomicslab

   Use when you have raw profile LC-MS data in .mzML format and need to prepare candidate peak regions for classification by a neural network detector (e.g., QuanFormer).
   2 installs
10. ▌
    Mass Spectrometry Chromatogram Generation · holobiomicslab

    Use when after MS2 annotation and sample alignment have been completed in JPA, when you need to visualize ion chromatograms for quality control, validate feature identities, or export chromatographic evidence for specific metabolic features across multiple samples.
    0 installs
11. ▌
    Mass Spectrometry Data Loader Integration · holobiomicslab

    Use when you have mass spectrometry data available in multiple identifier formats (GNPS Task ID, Universal Spectrum Identifier, or Feature-Based Molecular Networking task reference) and need to route each format to its specific loader without manual preprocessing.
    0 installs
12. ▌
    Mass Spectrometry Metadata Interpretation · holobiomicslab

    Use when when integrating LC-MS/MS data from diverse sources (e.g., public repositories like MSV000080102, instrument outputs, or precomputed workflows) into NPDtools pipelines.
    2 installs
13. ▌
    Mass Spectrometry Substructure Assignment · holobiomicslab

    Use when after Mass2Motif discovery via LDA on preprocessed MS/MS spectra, when you have a set of inferred motifs (fragments and neutral losses with LDA probabilities) and need to assign putative substructure identities rather than retain anonymous motif labels.
    2 installs
14. ▌
    Metabolite Feature Annotation Aggregation · holobiomicslab

    Use when after selecting statistically significant features from multi-assay LC-MS metabolomics datasets (e.g., via MB-VIP and permutation testing with p < 0.01).
    2 installs
15. ▌
    Metabolite Signal Extraction From Lc Hrms · holobiomicslab

    Use when you have raw untargeted LC/HRMS data (mzXML, mzML, or netCDF format) from population-scale studies (n > 500 samples) and need to extract a comprehensive peaklist with aligned features across all samples.
    2 installs
16. ▌
    Metabolomics Model Performance Comparison · holobiomicslab

    Use when you have trained multiple machine learning classifiers (e.g., AdaBoost, SVM, Random Forest) on the same metabolomics peak-quality training set using k-fold cross-validation with repeated runs (e.
    2 installs
17. ▌
    Metadata Normalization And Reconciliation · holobiomicslab

    Use when you have multiple CSV feature lists from different acquisition methods (e.g., LC-MS vs LC-IMS-MS) or processing software, each using different naming conventions, retention time scales, or m/z precision;
    0 installs
18. ▌
    Model Uncertainty Quantification Variance · holobiomicslab

    Use when when you have predictions from multiple independently trained models (e.g., ROASMI_1–ROASMI_5) for the same set of compounds in a reversed-phase liquid chromatography system at eluent pH ~2.7, and you need to estimate prediction reliability without ground-truth labels.
    2 installs
19. ▌
    Molecular Graph Neural Network Adaptation · holobiomicslab

    Use when you have an in-house collection of liquid chromatography spectra and retention time measurements for small molecules, and you want to improve structural identification accuracy by predicting retention times.
    2 installs
20. ▌
    Ms Spectra Inference With Neural Networks · holobiomicslab

    Use when you have MGF or native MS/MS arrays (mz_array, intensity_array, precursor_mz, adduct) and want to predict the most likely molecular formula. The input spectra must include required MGF fields (TITLE, PRECURSOR_MZ, PRECURSOR_TYPE, COLLISION_ENERGY) or equivalent Python API parameters.
    2 installs
21. ▌
    Ms2 Fragment M Z Grouping And Aggregation · holobiomicslab

    Use when you have extracted MS/MS spectra for a given metabolomic feature across multiple replicates (e.g., after top-TIC filtering) and need to identify which fragments are reproducible across replicates.
    0 installs
22. ▌
    Ms2 Spectral Deconvolution And Annotation · holobiomicslab

    Use when you have acquired LC-IMS-MS/MS data (or equivalent multidimensional MS/MS acquisition) in mzML or mzML.gz format and need to disambiguate overlapping fragmentation spectra arising from co-eluting or co-drifting precursor ions.
    0 installs
23. ▌
    Neural Network Model Inference Deployment · holobiomicslab

    Use when you have a pre-trained neural network model (e.g., MSBERT weights in .
    0 installs
24. ▌
    Pareto Front Multi Objective Optimization · holobiomicslab

    Use when you have evaluated a parametric denoising strategy (e.g., frequency-based filtering) at multiple threshold values and computed two or more competing metrics (e.g., signal loss and noise reduction) for each threshold.
    0 installs
25. ▌
    Post Translational Modification Detection · holobiomicslab

    Use when when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzML, mzXML, or mzData format) paired with either genome sequences or precursor peptide predictions, and you want to confirm the presence and identity of modified ribosomally synthesized and post-translationally modified.
    0 installs
26. ▌
    Probability Prediction Metric Computation · holobiomicslab

    Use when after running ModiFinder's probability generation on a known compound–modified compound pair, you have a vector of per-atom modification probabilities and need to validate whether the predicted probability peaks align with the true modification sites.
    0 installs
27. ▌
    Pseudo Ms Ms Spectra Ranking And Curation · holobiomicslab

    Use when after executing annotateRC to match six or more lipidomics/metabolomics features against ion fragment databases (e.
    0 installs
28. ▌
    Retention Time Mass Tolerance Calibration · holobiomicslab

    Use when you have multiple feature tables (CSV files) from different LC-MS analytical experiments, each containing mass, retention time, intensity, isotope, and adduct annotations, and you need to merge them into a single aligned feature matrix.
    2 installs
29. ▌
    Retention Time Prediction From Structures · holobiomicslab

    Use when you have molecular structures (SMILES or SDF format) for which you need to predict retention time in liquid chromatography, especially when your target dataset contains fewer than ~500 annotated examples.
    0 installs
30. ▌
    Sensitivity Specificity Tradeoff Analysis · holobiomicslab

    Use when you have a trained neural network model and a labelled validation dataset (with high-quality and low-quality peak annotations), and you need to determine the optimal probability threshold that maximizes the difference between true positive rate and false positive rate for classifying MS1.
    0 installs
31. ▌
    Siamese Network Architecture Modification · holobiomicslab

    Use when when you need to reduce overfitting in a Siamese neural network trained on mass spectrometry spectral pairs by adding weight regularization, or when users require flexible control over L1 and L2 penalty coefficients rather than hard-coded defaults.
    0 installs
32. ▌
    Signal Trend Assessment Across Injections · holobiomicslab

    Use when you have QCpool (pooled quality control) samples measured at regular intervals across one or more LC-MS/MS sequences and need to detect whether instrument performance degrades, drifts, or destabilizes during the analytical run.
    0 installs
33. ▌
    Singular Value Decomposition Metabolomics · holobiomicslab

    Use when when you have a log2-normalized, zero-mean, unit-variance intensity matrix (rows=metabolites, columns=samples) and a curated metabolite set database (e.
    0 installs
34. ▌
    Spectral Data Preprocessing Normalization · holobiomicslab

    Use when you have raw MS/MS spectral data in MGF format from multiple sources or instruments with inconsistent metadata fields, varying intensity scales, and potential low-quality spectra that need standardization before metadata harmonization or spectral library compilation.
    2 installs
35. ▌
    Spectral Document Representation Handling · holobiomicslab

    Use when you have per-sample MS2 spectra (in matchms-compatible formats like mzML, mzXML, MGF, or msp) and need to compare metabolomic samples across different LC methods, mass spectrometers, or retention-time regimes—especially when samples are chemodiverse with poor feature overlap or strong RT.
    0 installs
36. ▌
    Spectral Peak Detection And Deconvolution · holobiomicslab

    Use when you have raw LC-MS data in mzML or mzXML format and need to extract reproducible, high-quality metabolite features (m/z, retention time, intensity) for global metabolomics.
    0 installs
37. ▌
    Spectral Peak Filtering And Normalization · holobiomicslab

    Use when working with raw or minimally processed MS/MS spectra from repositories like GNPS that contain variable peak intensities, noise, and formatting inconsistencies that would interfere with downstream deep learning models trained on normalized spectral representations.
    0 installs
38. ▌
    Spectrum Processing Pipeline Construction · holobiomicslab

    Use when you have raw mass spectrometry spectra (in MGF, mzML, or similar formats) that must undergo standardized preprocessing before library matching, similarity searching, or performance benchmarking.
    0 installs
39. ▌
    Stable Isotope Probing Abundance Modeling · holobiomicslab

    Use when you have a high-resolution mass spectrum (FT scan) containing a peptide precursor at known charge state with known or suspected stable isotope labeling (e.
    2 installs
40. ▌
    Statistical Filtering Metabolite Features · holobiomicslab

    Use when when you have peak area tables (unlabeled C12 and labeled C13) from LC-MS metabolomics with sample metadata indicating case and control groups, and you need to distinguish true metabolic changes from instrumental noise or batch artifacts before attempting isotopic pairing.
    0 installs
41. ▌
    Summarized Experiment Object Construction · holobiomicslab

    Use when when you have imported a tab-delimited metabolomics file (via readData or similar) containing columns for compound identifiers, sample/aliquot names, peak areas (primary assay), internal standard areas (secondary assay), and sample type classifications, and you need to organize these into.
    0 installs
42. ▌
    Tandem Mass Spectra Fragmentation Parsing · holobiomicslab

    Use when when you have raw tandem mass spectra in mz/intensity format with precursor m/z values, and need to extract all fragmentation features (observed peaks and neutral losses) as a foundation for building interpretable machine learning models.
    2 installs
43. ▌
    Targeted Metabolomics Feature Elaboration · holobiomicslab

    Use when you have targeted metabolomics data with peak area intensities organized in rows (samples) × columns (compounds), accompanying sample metadata indicating which samples are blanks, calibration curve points, or QC samples with known concentration values, and a compound legend assigning.
    0 installs
44. ▌
    Tissue Specific Metabolite Quantification · holobiomicslab

    Use when you have LC-IM-MS/MS raw data from multiple tissue samples and need to identify and quantify unsaturated sterol lipids at the isomer level (distinguishing double-bond position and stereochemistry).
    0 installs
45. ▌
    Top N Accuracy And Auc Metric Calculation · holobiomicslab

    Use when you have a ranked candidate list (e.g., BGCs sorted by IOKR or strain-correlation score) for each test spectrum, a known ground-truth BGC for each spectrum, and you want to measure retrieval performance across multiple recall depths (top-1 through top-200) and overall discrimination.
    0 installs
46. ▌
    Transformer Encoder Architecture Training · holobiomicslab

    Use when you have paired tandem MS spectra and either (1) molecular fingerprints or structures as labels for supervised fingerprint prediction, or (2) both spectra and unpaired structure/SMILES libraries and want to train embeddings for database-free structure lookup.
    2 installs
47. ▌
    Unmatched Peak Detection And Penalization · holobiomicslab

    Use when when annotating MS/MS spectra against spectral libraries and chimeric spectra (spectra containing fragments from multiple precursor ions) are suspected or known to be present in your dataset.
    2 installs
48. ▌
    Wmy Network Prediction Confidence Scoring · holobiomicslab

    Use when after initial lipid candidate annotation via spectral library matching (e.g., from XCMS/CAMERA peak alignment and LipidIN EQ module querying), when you need to improve coverage and annotation confidence on unannotated or low-confidence lipid signals.
    0 installs
49. ▌
    Coefficient Of Variation Threshold Analysis · holobiomicslab

    Use when you have per-feature CV values from quality control analysis of NMR or MS metabolomic data and need to: (1) establish whether your dataset meets FDA reproducibility standards for downstream biomarker discovery or quantification; (2) benchmark data quality against regulatory thresholds;
    0 installs
50. ▌
    Compound Abundance Quantification From Flow · holobiomicslab

    Use when you have an NMR mixture spectrum (1D or 2D) and a library of reference spectra for pure compounds, and you need to identify which compounds are present and in what proportions.
    0 installs
51. ▌
    Compound Clustering From Inadequate Spectra · holobiomicslab

    Use when after peak picking has identified individual signals in an INADEQUATE NMR spectrum, apply this skill when you need to collapse thousands of individual peaks into fewer, more interpretable compound-level peak networks.
    0 installs
52. ▌
    Data Pipeline Module Design And Integration · holobiomicslab

    Use when you have raw spectroscopic datasets from heterogeneous sources (multiple Zenodo repositories with different file formats and scales) that must be jointly normalized, deduplicated, and aligned by molecular identifier to feed a multimodal deep learning architecture.
    0 installs
53. ▌
    HTTP API Integration With External Services · holobiomicslab

    Use when when your application needs to enrich or predict spectral properties (NMR peaks, molecular structure) by querying external databases, and you have peak data (chemical shift, multiplicity, integration) that must be transformed into a remote service's query format, validated, and the.
    0 installs
54. ▌
    Molecular Structure Prediction From Spectra · holobiomicslab

    Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra (as numerical arrays or feature tensors) from an unknown organic compound with ≤19 heavy atoms, and you need to predict both the molecular formula and the connectivity graph of the compound without prior structural hypotheses or reference.
    0 installs
55. ▌
    Spectral Overview Representation Generation · holobiomicslab

    Use when you have processed LC-MS/MS spectral data (as a .mgf file with feature identifiers) and computed pairwise ms2deepscore similarity scores, and you need to create a 2-D projection suitable for dashboard visualization or high-level pattern discovery without losing similarity structure.
    0 installs
56. ▌
    Spectral Similarity Matching And Comparison · holobiomicslab

    Use when after extracting and optionally combining MS2 spectra from a chromatographic peak (e.g., at a known m/z value like 304.1131), you need to determine which compound(s) in a reference library match the experimental spectrum.
    2 installs
57. ▌
    Bam File Coordinate Sorting Verification · holobiomicslab

    Use when before invoking pp.make_fragment_file on a BAM file from alignment or external sources, especially when the BAM's sort order is unknown or when integrating BAM files from multiple sequencing platforms (10X, standard genomics pipelines, or custom aligners) into a unified SnapATAC2 analysis.
    0 installs
58. ▌
    Dependency Installation And Verification · holobiomicslab

    Use when when setting up HiC-Pro or similar multi-tool pipelines where tool availability and version constraints are prerequisites for downstream analysis.
    0 installs
59. ▌
    Dna Methylation Block Detection Analysis · holobiomicslab

    Use when you have loaded normalized methylation data from EPIC or 450k arrays and need to identify differentially methylated blocks rather than individual CpG sites or DMRs.
    0 installs
60. ▌
    Fragment Length Prediction And Extension · holobiomicslab

    Use when after filtering duplicate reads from ChIP-Seq data but before generating pileup coverage tracks.
    0 installs
61. ▌
    Hi C Matrix Normalization Pipeline Setup · holobiomicslab

    Use when before running HiC-Pro's normalization stage on aligned Hi-C BAM files. Specifically, when you have SAM/BAM-formatted aligned Hi-C reads that need bias correction and matrix balancing to produce normalized contact maps suitable for downstream chromatin structure analysis.
    0 installs
62. ▌
    Illumina Methylation Array Preprocessing · holobiomicslab

    Use when your input is raw .idat files or a beta-valued matrix from Illumina HumanMethylation450 or EPIC arrays, and you need to remove unreliable probes (those with detection p-value > 0.01 or insufficient bead counts) before performing differential methylation or other downstream analyses.
    0 installs
63. ▌
    Kilobase Resolution Contact Map Analysis · holobiomicslab

    Use when you have paired-end Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited) and need to produce standardized .hic binary contact maps that conform to ENCODE reference formats and integrity standards for downstream 3D genome analysis.
    0 installs
64. ▌
    Nucleotide Footprint Pattern Recognition · holobiomicslab

    Use when you have aligned ATAC-seq BAM files and want to discriminate between transcription factor binding sites that are actually occupied by protein versus sites with matching sequence motifs that are unbound.
    0 installs
65. ▌
    Statistical Overlap Proportion Reporting · holobiomicslab

    Use when after identifying differentially methylated bases (q-value < 0.01, methylation difference > 25%) using calculateDiffMeth(), use this skill to determine what fraction of those bases overlap with specific gene features (promoters, exons, introns) and CpG contexts (islands vs. shores).
    0 installs
66. ▌
    Binary Stream Seeking And Decompression · holobiomicslab

    Use when you have a large gzip-compressed file (e.g., mzML.gz) with an embedded index structure in the gzip header comment field, and you need to retrieve specific blocks (e.g., mass spectra by scan number, chapters by ID) without decompressing the entire file.
    0 installs
67. ▌
    Build Artifact Retrieval And Validation · holobiomicslab

    Use when when you need to verify that a GitHub Actions workflow (such as dev_build_release.
    1 install
68. ▌
    Domain Specific Language Grammar Design · holobiomicslab

    Use when when you need to enable non-programmers or domain experts to formulate complex, unambiguous queries over specialized data (e.
    2 installs
69. ▌
    Tanaka Physicochemical Descriptor Handling · holobiomicslab

    Use when you have raw HPLC column metadata arrays containing Tanaka parameter blocks that will be fed into a featurizer for machine learning on retention times. Tanaka parameters are present but may contain string artifacts ('2.7 spp', '2.
    0 installs
70. ▌
    Tandem Ms Feature Table Import And Parsing · holobiomicslab

    Use when when you have raw feature tables exported from a tandem LC-MS/MS preprocessing tool (e.g., Progenesis QI, MS-DIAL, Bruker Metaboscape) and need to combine them with sample metadata (group assignments, replicate structure) before applying feature filtering or quality control workflows.
    0 installs
71. ▌
    Tanimoto Similarity Scoring Implementation · holobiomicslab

    Use when when you have paired mass spectrometry spectra (e.g., from GNPS, MoNA, MassBank, or MSnLib) and need to predict continuous structural similarity scores (0–1 range) between them, especially when traditional spectral-distance metrics (e.
    0 installs
72. ▌
    Topic Modeling Hyperparameter Optimization · holobiomicslab

    Use when when preparing to apply LDA to a new MS/MS spectral dataset in bag-of-fragments format, before running the full modeling pipeline.
    2 installs
73. ▌
    Training Validation Dataset Stratification · holobiomicslab

    Use when when you have a complete labelled MS/MS spectral dataset annotated as 'relevant' (compounds of interest from reference standards) or 'other' (reference standards or non-target compounds from repositories), and you need to train and evaluate an AnnoMe binary classifier without data leakage.
    0 installs
74. ▌
    Type Safety And Length Matching Validation · holobiomicslab

    Use when implementing data replacement methods (such as `[<-`, `$<-`, `mz<-`, `intensity<-`, `peaksData<-`) in a writable MsBackend subclass.
    0 installs
75. ▌
    Vendor Proprietary Format Interoperability · holobiomicslab

    Use when you have mass spectrometry raw data in a proprietary vendor format (Thermo .raw, Agilent .d with or without ion mobility, Bruker ion mobility .d, or mzML) and need to enable reproducible, language-agnostic access to multidimensional spectra (e.
    0 installs
76. ▌
    Accurate Mass Metabolite Search Against Hmdb · holobiomicslab

    Use when after MS1 feature detection and spectra merging in an untargeted or semi-targeted metabolomics workflow, when you have a list of observed accurate m/z values from high-resolution mass spectrometry (e.
    0 installs
77. ▌
    Bi Encoder Cross Encoder Architecture Design · holobiomicslab

    Use when you have paired spectrum-compound reference data and need to simultaneously retrieve candidate compounds rapidly (bi-encoder) while also refining relevance scores through joint context modeling (cross-encoder).
    0 installs
78. ▌
    Blood Sample Processing Parameter Extraction · holobiomicslab

    Use when when you have peripheral blood sample cohorts (plasma/serum) with multiple timestamps (e.
    0 installs
79. ▌
    Metabolite Concentration To Spectrum Mapping · holobiomicslab

    Use when when you have a list of known metabolite concentrations and their corresponding J-coupling constants (spin systems) and need to generate realistic 1D 1H NMR spectra or 2D correlation spectra (COSY, HSQC, HMQC) for simulation, validation, or educational purposes, without access to actual.
    0 installs
80. ▌
    Molecular Transformation Frequency Filtering · holobiomicslab

    Use when after clustering pairwise mass differences into transformation groups from FT-ICR MS formula-assigned datasets, apply this skill when you have a catalog of transformation pairs (e.
    2 installs
81. ▌
    Nmr Network Visualization And Interpretation · holobiomicslab

    Use when you have 2D NMR spectra (heteronuclear: HSQC, HMBC;
    0 installs
82. ▌
    Transformer Model Inference On Spectral Data · holobiomicslab

    Use when you have a 1D 1H NMR spectrum represented as chemical shift vs. intensity values, a corresponding list of detected peak positions, and you need to assign metabolite identities to those peaks.
    0 installs
83. ▌
    Bootstrap Confidence Interval Computation · holobiomicslab

    Use when when you have computed z-score deviations for genomic annotations (e.g., motifs) across multiple cells or samples and need to quantify uncertainty in their variability rankings before performing differential or comparative analyses.
    0 installs
84. ▌
    Checksum Verification For Reproducibility · holobiomicslab

    Use when you have executed a complex multi-step processing pipeline (e.g., ENCODE Hi-C uniform processing pipeline) and need to confirm that the generated output files match a known reference baseline.
    0 installs
85. ▌
    Conda Environment Creation And Management · holobiomicslab

    Use when you need to deploy a complex multi-language pipeline (e.g., HiC-Pro) that requires Python >3.7 libraries (pysam, bx-python, numpy, scipy), R packages (ggplot2, RColorBrewer), and compiled tool binaries (bowtie2, samtools >=1.
    0 installs
86. ▌
    Differential Accessibility Interpretation · holobiomicslab

    Use when after identifying differentially accessible peaks (via tl.
    0 installs
87. ▌
    Leiden Clustering Resolution Optimization · holobiomicslab

    Use when you have performed spectral dimension reduction on single-cell omics count matrices and wish to partition cells into discrete populations.
    0 installs
88. ▌
    Makefile Based Build System Configuration · holobiomicslab

    Use when when deploying a complex bioinformatics pipeline (e.g., HiC-Pro) that depends on multiple external tools with version constraints (samtools ≥1.9, bowtie2, R packages, Python libraries) and you need to verify their availability and configure their paths before running the analysis.
    0 installs
89. ▌
    Multiome Data Ingestion Paired Modalities · holobiomicslab

    Use when you have independently generated or received both scATAC-seq peak count matrices and scRNA-seq gene expression matrices from the same set of cells (multiome experiment), and you need to perform joint analysis such as co-clustering, trajectory inference, or regulatory inference that.
    0 installs
90. ▌
    Rna Seq Expression Alignment Across Cells · holobiomicslab

    Use when you have paired scATAC-seq and scRNA-seq data from the same cells (multiome experiment) and want to perform integrated analysis that leverages both chromatin accessibility and gene expression signals.
    0 installs
91. ▌
    Activity Score Computation And Reporting · holobiomicslab

    Use when you have preprocessed metabolite intensity data (log2-transformed, zero-mean unit-variance standardized) mapped to compound annotations, and you need to derive activity scores for a set of metabolite groups (pathways, Molecular Families, Mass2Motifs, or custom metabolite sets) to rank them.
    0 installs
92. ▌
    Comparative Enrichment Method Evaluation · holobiomicslab

    Use when you are selecting a pathway enrichment method for metabolomics peak data and need to assess which method will remain stable when your data contains noise, dropout, or missing identifications.
    0 installs
93. ▌
    Computational Execution Table Generation · holobiomicslab

    Use when when you have a set of gallery or benchmark scripts (e.
    0 installs
94. ▌
    Consensus Clustering Algorithm Selection · holobiomicslab

    Use when when you have computed hierarchical clustering dendrograms on your feature matrix (microbes or metabolites) using Euclidean distance and complete linkage, and need to determine how many clusters to cut the dendrogram into.
    0 installs
95. ▌
    Contrastive Learning Loss Implementation · holobiomicslab

    Use when when you have paired augmented ion images processed through ResNet18 encoders producing 512-dimensional representation vectors, and you need to learn meaningful low-dimensional representations without labeled data by enforcing that augmentations of the same image remain similar while.
    0 installs
96. ▌
    Custom File Wrapper Class Implementation · holobiomicslab

    Use when when you have mass spectrometry data stored in a database or non-mzML file format and need to integrate it into the pymzML pipeline without converting to mzML. Use this skill when FileInterface does not natively recognize your file extension and you want to avoid data conversion overhead.
    0 installs
97. ▌
    Deep Neural Network Latent Space Mapping · holobiomicslab

    Use when you have a pre-trained DNN model for retention time prediction and need to adapt it to a new chromatographic method or instrument where you have only 10–20 calibration molecules with known retention times;
    2 installs
98. ▌
    Documentation And Metadata Modernization · holobiomicslab

    Use when a mature scientific package (e.g., Mummichog 3) is being migrated to a new GitHub organization that enforces standardized project structure, and the current setup.py, pyproject.toml, requirements.txt, .
    0 installs
99. ▌
    Error Metric Comparison And Benchmarking · holobiomicslab

    Use when you have predicted retention times from one or more machine learning models (DNN, Gaussian Process, or ensemble) applied to small-molecule chromatography data, along with corresponding experimental ground-truth retention times, and need to quantify prediction accuracy and rank competing.
    0 installs
100. ▌
     File Handler Instantiation And Lifecycle · holobiomicslab

     Use when you need to open an mzML file in pymzML and must automatically select the correct handler based on file extension (.mzML, .mzML.gz, .db) and—for gzip files—indexed vs. non-indexed compression status. Use it whenever FileInterface.
     0 installs