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HolobiomicsLab

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1. ▌
   Scoring Function Sensitivity Analysis · holobiomicslab

   Use when you have two or more complementary scoring functions (e.g., strain correlation and IOKR scores) that you wish to combine, and you need to determine which combination strategy and parameters maximize enrichment of known true links in a validation set.
   0 installs
2. ▌
   Shell Scripting For Program Discovery · holobiomicslab

   Use when a scientific application (such as QCxMS2) requires multiple external programs with specific version constraints and you need to programmatically verify their presence and compatibility before executing calculations.
   0 installs
3. ▌
   Sinusoidal Positional Encoding Design · holobiomicslab

   Use when you have variable-length lists of MS/MS peaks (m/z and intensity pairs) that need to be encoded into a fixed-dimensional representation compatible with transformer architecture.
   0 installs
4. ▌
   Sparse Distance Matrix Interpretation · holobiomicslab

   Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes (containing only cosine distances between neighboring spectra, not exhaustive pairwise comparisons) and need to partition spectra into groups of similar ions or peptides.
   0 installs
5. ▌
   Spectral Data Loading From Repository · holobiomicslab

   Use when when you need to retrieve a specific MS/MS spectrum from a public proteomics repository (PRIDE, MassIVE, PeptideAtlas) by its USI string for annotation, visualization, or comparative analysis, rather than working with locally stored mzML/mzXML files or already-loaded spectrum objects.
   0 installs
6. ▌
   Spectral Fragmentation Motif Analysis · holobiomicslab

   Use when when you have metabolomics intensity data with metabolites grouped by fragmentation spectral similarity (Molecular Families or Mass2Motifs) and need to rank or score these groups by their differential activity across experimental conditions, especially when traditional pathway databases.
   0 installs
7. ▌
   Spectral Library Integration Workflow · holobiomicslab

   Use when when you have experimental UHPLC-HRMS/MS data targeting lipid species not adequately covered by LipidMatch's built-in library (500,000+ species across 60+ lipid types), or when working with specialized applications requiring custom lipid definitions (e.
   0 installs
8. ▌
   Spectral Library Match Classification · holobiomicslab

   Use when when you have run MS2Query on query MS/MS spectra and obtained results with library matches that need to be disambiguated into two categories: (1) exact matches (precursor m/z difference near zero) versus (2) analog matches (chemically related but different precursor m/z).
   0 installs
9. ▌
   Spectral Network Propagation Analysis · holobiomicslab

   Use when after running MetaMiner's Dereplicator stage to identify some RiPPs via direct database matching against a constructed structure database, apply this skill to enlarge the set of identifications by propagating those matches through spectral clusters and visualizing the connected components.
   0 installs
10. ▌
    Spectral Peak Detection Composite Map · holobiomicslab

    Use when when you have aligned mass tracks (extracted ion chromatograms) across multiple LC-MS samples consolidated into a composite map and need to detect reproducible elution peaks (features) that will be tracked back to individual samples.
    0 installs
11. ▌
    Spectral Peak Grouping Mass Tolerance · holobiomicslab

    Use when after extracting raw MS/MS spectra from mzML files when you observe high fragment counts per spectrum (e.g., 98 fragments) and want to reduce noise from instrument measurement uncertainty.
    0 installs
12. ▌
    Spectral Peak Intensity Normalization · holobiomicslab

    Use when after loading raw m/z peak data (in MetaboAnalyst, MetaboShiny native, or Metabolights format) and merging it with sample metadata (batch IDs, concentration values, experimental group labels).
    0 installs
13. ▌
    Spectral Peak Matching With Tolerance · holobiomicslab

    Use when when comparing a query MS/MS spectrum (e.g., from an unknown metabolite) against a library spectrum to establish correspondence between peaks. Use this skill before calculating similarity scores (cosine, entropy, Bhattacharyya) or when applying penalty factors to unmatched peaks.
    0 installs
14. ▌
    Spectral Quality Assurance Proteomics · holobiomicslab

    Use when when you have extracted a raw Orbitrap scan from a .raw file and need to verify that the instrument operated within expected parameters and that observed peptide fragment ions rise substantially above noise—i.
    0 installs
15. ▌
    Spectral Similarity Score Computation · holobiomicslab

    Use when when you have pairs of MS/MS spectra (in mgf, msp, mzml, mzxml, json, or usi format) and need to retrieve structurally related compounds or rank spectral similarity on a continuous scale (Tanimoto prediction).
    0 installs
16. ▌
    Standalone Web Application Deployment · holobiomicslab

    Use when you have cloned the GNPS_MASST codebase and need to instantiate a domain-specific MASST variant (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, or foodMASST) to accept individual MS/MS spectra as input queries and perform searches against the corresponding curated reference.
    0 installs
17. ▌
    Statistical Visualization Multi Group · holobiomicslab

    Use when when you have loaded search results from two or more DIA-MS analysis tools (e.
    0 installs
18. ▌
    Subformula Assignment Neural Networks · holobiomicslab

    Use when when you have MS/MS spectra with assigned precursor formulas and need to annotate fragment peaks with their chemical subformulas, but want to avoid the computational overhead of generating full SIRIUS fragmentation trees or do not have access to spectrum databases.
    0 installs
19. ▌
    Substrate Concentration Normalization · holobiomicslab

    Use when you have LC-MS normalized intracellular metabolite abundance data from multiple cell lines (or samples) and need to compute reaction-level propensity scores that account for substrate availability as a predictor of metabolic flux.
    0 installs
20. ▌
    Tanimoto Score Threshold Optimization · holobiomicslab

    Use when when you have a set of MS/MS spectra with ground-truth structural similarity labels (Tanimoto scores computed from molecular fingerprints) and need to choose a decision threshold for classifying spectrum pairs as 'chemically related' or 'unrelated'.
    0 installs
21. ▌
    Targeted Feature Extraction From Lcms · holobiomicslab

    Use when you have a curated target list of m/z values, retention times, and identifiers for specific metabolites of interest, and you want to extract only those features from LC-MS data (mzML or netCDF format) rather than performing untargeted feature discovery.
    0 installs
22. ▌
    Targeted Proteomics Feature Filtering · holobiomicslab

    Use when you have loaded transition group chromatogram data from sqMass files and need to restrict the analyte selection dropdowns (protein, peptide, charge state) to only those features passing a specified Q-value threshold (default 1%), or when you need to selectively display or hide MS1 and MS2.
    0 installs
23. ▌
    Tensor Operation Element Wise Product · holobiomicslab

    Use when you have two embedding tensors of identical shape (e.g., both 512-dimensional) and need to produce a fused representation that captures multiplicative interactions between modalities.
    0 installs
24. ▌
    Threshold Based Sample Classification · holobiomicslab

    Use when after normalization (step 7) in untargeted metabolomic profiling pipelines, when you have a preprocessed feature matrix and need to identify samples with anomalous metabolic profiles that violate multivariate assumptions or represent technical failures.
    0 installs
25. ▌
    Ms1 Feature Peak Detection In Full Scan · holobiomicslab

    Use when you have merged MS1 spectra (output from spectral binning/merging steps) from a full-scan FIA-MS or LC-MS acquisition and need to identify distinct molecular features before accurate mass annotation or background filtering.
    0 installs
26. ▌
    Natural Product Classifier Substitution · holobiomicslab

    Use when gNPS has ceased supplying ClassyFire ontology information for spectral library matches, causing downstream ConCISE consensus classification to fail or produce incomplete ontology fields.
    0 installs
27. ▌
    Natural Products Workflow Orchestration · holobiomicslab

    Use when you have LC-MS/MS DDA metabolomics data (positive and/or negative ionization modes) and sample metadata (originating taxon) for one or more samples, and you need to generate a Wikidata-connected RDF knowledge graph for integrated natural products analysis, taxonomy-aware compound.
    0 installs
28. ▌
    Network Based Metabolite Identification · holobiomicslab

    Use when when you have m/z values from spatially-resolved mass spectrometry imaging (MSI) and need to predict their molecular formulae with high precision.
    0 installs
29. ▌
    Network Graph Re Annotation Propagation · holobiomicslab

    Use when when you have completed an initial ModiFinder analysis on a compound pair (known compound + modified analog with unknown structure), and you subsequently acquire or determine the structure of the modified compound.
    0 installs
30. ▌
    Nontargeted Analysis Workflow Execution · holobiomicslab

    Use when you have UPLC-HRMS data from ThermoFisher, Agilent, or other vendor instruments (converted via MSConvert if needed), organized as batch-processed files ready for MSThunder input, and you need to identify unknown organic pollutants with deep learning-assisted structure prediction and.
    0 installs
31. ▌
    Numpress Compression Algorithm Encoding · holobiomicslab

    Use when you have raw floating-point m/z and intensity arrays extracted from mass-spectrometry experiments (e.g., from mzML or mzXML files) and need to compress them for storage or transmission.
    0 installs
32. ▌
    Parental Signal Selection From Clusters · holobiomicslab

    Use when after feature clustering has grouped LC-MS peaks by MS-DIAL peak character estimation, you need to reduce the cluster to a single representative feature per biological entity.
    0 installs
33. ▌
    Peak Boundary Definition And Validation · holobiomicslab

    Use when after nontargeted peak detection has identified candidate peaks in LC-MS chromatograms, when you need to establish exact peak start/end retention times and extract peak-level metadata (intensity, width, shape) for downstream feature quality evaluation and annotation workflows.
    0 installs
34. ▌
    Peak Intensity Removal And Thresholding · holobiomicslab

    Use when when you have imported raw mass spectrometry spectral data (in formats like mzML, mzXML, msp, MGF, or JSON) and need to clean peak lists before metadata validation, similarity scoring, or library comparison.
    0 installs
35. ▌
    Peak To Metabolite Candidate Assignment · holobiomicslab

    Use when you have a raw peak-intensity matrix from untargeted LC-MS data (organized as rows=peaks, columns=samples) and need to generate initial candidate metabolite assignments.
    0 installs
36. ▌
    Peptide B Y Ion Theoretical Calculation · holobiomicslab

    Use when when you have a peptide sequence and need to predict which fragment ions (B and Y series) should appear in an MS2 spectrum at a known isotopic abundance (e.g., natural 13C at 1.07%, or stable isotope labeling at 50% enrichment).
    0 installs
37. ▌
    Peptide Sequence To Spectrum Conversion · holobiomicslab

    Use when when you have a peptide sequence and need to predict its fragmentation pattern under specific isotopic labeling conditions (e.g., natural 13C abundance at 1%, or enriched 13C at arbitrary levels).
    0 installs
38. ▌
    Per Sample Feature Composition Analysis · holobiomicslab

    Use when when you have aligned and quantified mass spectrometry features from multiple natural extracts (via MZmine2/3), paired with in silico annotation results (ISDB or SIRIUS), and you need to prioritize samples for chemical discovery based on the proportion of unannotated, extract-specific.
    0 installs
39. ▌
    Podp Metadata Retrieval And Integration · holobiomicslab

    Use when when running NPLinker in PODP mode (as opposed to local mode), you need to fetch and validate project metadata from PODP, orchestrate downloads of GNPS molecular networking data, AntiSMASH BGC predictions, BigScape clustering results, and MIBiG reference metadata, then organize them into.
    0 installs
40. ▌
    Precursor Mass Neutral Loss Calculation · holobiomicslab

    Use when when analyzing tandem mass spectra (MS/MS data) and you want to incorporate neutral loss patterns—characteristic mass losses from molecular precursors—into your spectral similarity or feature representation.
    0 installs
41. ▌
    Pytorch Model Training And Optimization · holobiomicslab

    Use when when you have preprocessed molecular graph representations (from Preprocess.py or equivalent) and need to train a regression model to predict continuous retention time targets.
    0 installs
42. ▌
    Quality Assurance Contamination Removal · holobiomicslab

    Use when you have a feature quantification table exported from MZmine3 processing of non-targeted LC-MS/MS data that includes both biological samples and blank/control samples, and you need to identify and exclude features whose intensity is driven by contamination in blanks rather than true.
    0 installs
43. ▌
    Quantum Chemistry Structure Preparation · holobiomicslab

    Use when when you have a collection of N-Me derived unsaturated sterol lipid identifiers or structures and need to generate predicted collision cross section (CCS) values for LC-IM-MS/MS analysis.
    0 installs
44. ▌
    Quantum Mechanical Property Calculation · holobiomicslab

    Use when when you have interpolated or optimized molecular geometries (from geodesic_interpolate or CREST conformer ensembles) and need to compute ab initio electronic energies, orbital properties, or transition state characteristics to populate a fragmentation reaction network or validate.
    0 installs
45. ▌
    Retention Time Correction And Alignment · holobiomicslab

    Use when you have multiple LC-MS runs with the same set of targets (compounds) and observe or expect retention time drift or jitter between runs.
    0 installs
46. ▌
    Roi Tensor Formatting For Deep Learning · holobiomicslab

    Use when after segmenting raw profile LC-MS data into candidate ROIs containing potential peaks, and before feeding ROI data to a CNN-Transformer peak detection network.
    0 installs
47. ▌
    Rt Transformation Parameter Calculation · holobiomicslab

    Use when you have centroided mzML or mzXML LC-MS files from a single batch run that exhibit systematic retention-time drift between samples, one or more designated QC reference file(s), and you need to harmonize RT coordinates across all samples before feature detection to reduce false positive and.
    0 installs
48. ▌
    S4 Class Definition And Slot Management · holobiomicslab

    Use when you are extending the MsBackend virtual class to create a new backend for storing MS spectra data and need to define the internal data structure. Specifically: when you have multiple types of spectra variables (e.
    0 installs
49. ▌
    Siamese Architecture Module Integration · holobiomicslab

    Use when when refactoring a mass-spectrometry formula-prediction codebase that has deprecated a monolithic scoring function (FDRNet) and requires a modular, symmetric Siamese design to independently embed spectrum and molecular-formula features before combining them.
    0 installs
50. ▌
    Signal To Noise Ratio Calculation Peaks · holobiomicslab

    Use when after elution peaks have been detected on composite mass tracks using local maxima and prominence detection, before reporting features in the final feature table.
    0 installs
51. ▌
    Sparse Vs Dense Vector Format Selection · holobiomicslab

    Use when when converting high-resolution tandem mass spectra to vectors for clustering or similarity searching, you must decide whether to output sparse or dense vectors. Use this decision point after binning spectra into mass bins but before constructing nearest-neighbor indexes.
    0 installs
52. ▌
    Spatial Metabolomics Feature Annotation · holobiomicslab

    Use when your spatial metabolomics dataset contains raw m/z features (e.g., from MALDI-MS imaging or LC-MS/MS) without metabolite annotations, and you have selected a reference database and adduct type appropriate for your ionization mode and biological sample.
    0 installs
53. ▌
    Spectral Data Input Handling Mgf Format · holobiomicslab

    Use when when you have raw MS/MS mass spectrometry data and need to submit it to the Mass2SMILES Docker inference container for structure and functional group prediction.
    0 installs
54. ▌
    Spectral Data Normalization And Merging · holobiomicslab

    Use when you have acquired multiple MS1 spectra over a defined acquisition time range (e.g., 0–30 s in FIA-MS) and need to combine them into a unified spectrum before feature detection.
    0 installs
55. ▌
    Spectral Data Processing And Annotation · holobiomicslab

    Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular features, build a molecular network from fragmentation spectra, and annotate those features using both spectral.
    0 installs
56. ▌
    Spectral Entropy Similarity Computation · holobiomicslab

    Use when you need to measure the similarity between two MS/MS spectra as a continuous value that reflects both peak presence/absence and intensity patterns, particularly when comparing noisy versus denoised spectrum variants, or when ranking candidate reference library matches during compound.
    0 installs
57. ▌
    Spectral Feature Scrambling Permutation · holobiomicslab

    Use when when performing large-scale untargeted metabolomics annotations where you need to assess the false discovery rate of metabolite identifications but lack sufficient negative control samples or decoy compound databases.
    0 installs
58. ▌
    Spectral Library Matching With Taxonomy · holobiomicslab

    Use when you have MS/MS spectra (.mgf) and candidate metabolite annotations (with m/z, retention time, chemical identifiers) linked to a known organism or taxon, and you want to rank annotations by both spectral similarity AND biochemical likelihood in that organism's lineage.
    0 installs
59. ▌
    Spectral Motif Inference And Extraction · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (converted to bag-of-fragments format with neutral losses extracted and noise filtered) and seek to identify recurring fragmentation patterns indicative of molecular substructures across a spectral cohort.
    0 installs
60. ▌
    Spectral Overlay Rendering Multi Sample · holobiomicslab

    Use when when you have aligned peak-alignment data from a preceding molecular networking task (structured as a table with peak intensity, m/z, retention time, and alignment quality metrics) and need to visualize and interactively filter peaks across multiple spectra to support comparative mass.
    0 installs
61. ▌
    Spectral Peak Annotation Using Proforma · holobiomicslab

    Use when you have a tandem mass spectrum with observed m/z peaks and a known peptide sequence (as a ProForma string, optionally with post-translational modifications), and you want to determine which observed peaks correspond to expected fragment ions (b-type, y-type, a-type) within a specified.
    0 installs
62. ▌
    Spectral Peak Binning And Vectorization · holobiomicslab

    Use when you have raw MS/MS spectra with variable numbers of peaks at continuous m/z values and need to feed them to a neural network (e.g., Siamese network for similarity prediction) that requires fixed-size vector input.
    0 installs
63. ▌
    Spectral Similarity Matching Algorithms · holobiomicslab

    Use when when you have experimental MS/MS spectra (from mzML or .rda preprocessed format) and need to annotate them against a reference fragmentation library.
    0 installs
64. ▌
    Spectral Similarity Scoring And Ranking · holobiomicslab

    Use when after discovering Mass2Motifs via LDA topic modeling on MS/MS data, when you need to assign putative structural annotations to those motifs by comparing their fragmentation signatures (weighted fragment and neutral loss distributions) to a curated reference database of known motifs and.
    0 installs
65. ▌
    Spectrum Feature Engineering Validation · holobiomicslab

    Use when when implementing or auditing a deep learning pipeline for MS/MS-based molecular formula prediction, verify that precursor m/z values in the input feature array are zeroed before they reach the spectrum encoder (e.g., TCN).
    0 installs
66. ▌
    Structural Cluster Network Construction · holobiomicslab

    Use when after you have identified statistically significant LC-MS features and run MamsiStructSearch to generate structural clusters (isotopologue groups, adduct groups, cross-assay links) and computed correlation cluster assignments.
    0 installs
67. ▌
    Tab Delimited Metabolomics File Parsing · holobiomicslab

    Use when when you have raw metabolomics measurements in tab-delimited text format (e.g., from Sciex OS exports) and need to load them into R for quality control analysis.
    0 installs
68. ▌
    Targeted Peak Integration Configuration · holobiomicslab

    Use when when performing targeted quantification of known compounds in LC-MS data using TARDIS, especially when the instrument acquired data with multiple overlapping m/z scan windows.
    0 installs
69. ▌
    Tensorflow Cpu Runtime Parameter Tuning · holobiomicslab

    Use when deploying Mass2SMILES on a TensorFlow-CPU build and you need to optimize inference throughput on multi-core systems. This is particularly necessary when GPU inference is unavailable due to CUDA driver incompatibility, or when inference hardware has variable core counts (e.
    0 installs
70. ▌
    Tof Ms Signal Enhancement Low Abundance · holobiomicslab

    Use when your raw TOF-MS data (Agilent MassHunter .d format) exhibits jagged, artifact-prone peaks in low-abundance ions that compromise peak quality assessment or when you need to improve signal-to-noise before ion mobility demultiplexing or peak deconvolution.
    0 installs
71. ▌
    Training Data Loading And Preprocessing · holobiomicslab

    Use when you have downloaded raw LC-MS spectral peak data from a public repository (e.g., DOI 10.25345/C5FD2F) and need to ingest it into memory and prepare it in the format expected by a TensorFlow/Keras neural network classifier.
    0 installs
72. ▌
    Training Validation Test Set Allocation · holobiomicslab

    Use when after labeling a representative subset of peaks (typically 10–20 pooled samples with corresponding feature tables) and before neural network training, when you need to split labeled data into independent subsets for model training, hyperparameter tuning, and unbiased performance evaluation.
    0 installs
73. ▌
    Transformer Architecture Implementation · holobiomicslab

    Use when when building a neural network to map between mass spectrometry spectra and molecular properties (e.g., fingerprints, SMILES, or fragment ions) where sequential or spectral feature dependencies must be captured.
    0 installs
74. ▌
    Transformer Encoder Architecture Design · holobiomicslab

    Use when when you need to learn chemical-rational embeddings of tandem MS/MS spectra for library matching or molecular property prediction, and you want to leverage self-supervised learning through masking.
    0 installs
75. ▌
    Tsne Embedding Dimensionality Reduction · holobiomicslab

    Use when when you have a precomputed similarity matrix of mass spectra (e.
    0 installs
76. ▌
    Untargeted Metabolomics Data Processing · holobiomicslab

    Use when you have untargeted MS2 spectral data (from LC-MS/MS or similar instruments) and need to assign metabolic pathway context to detected compounds when standard spectral library matching is unavailable or insufficient.
    0 installs
77. ▌
    Virtual Mass Spectrometer Configuration · holobiomicslab

    Use when when you have generated or extracted a chemical mixture (via DatabaseFormulaSampler, ChemicalMixtureCreator, or ChemicalMixtureFromMZML) and need to establish a virtual instrument to simulate scan acquisition.
    0 installs
78. ▌
    Block Layout Analysis For Io Optimization · holobiomicslab

    Use when when preparing NMR datasets for processing in NMRFx and the Dataset.createDataFile() method must choose among competing storage backends.
    0 installs
79. ▌
    Convolutional Neural Network Layer Design · holobiomicslab

    Use when you have 1H NMR spectral tensors as input and need to extract local features (e.g., peak patterns, signal neighborhoods) before applying attention-based or sequence-level processing.
    0 installs
80. ▌
    Fragment Ion Theoretical Mass Calculation · holobiomicslab

    Use when when building a comprehensive lipid fragment ion library covering all chain composition and positional isomer variants (e.g., 168.6 million entries).
    0 installs
81. ▌
    Graph Neural Network Design For Chemistry · holobiomicslab

    Use when you have 1D or 2D NMR spectra (1H and/or 13C) and need to predict unknown molecular structure (formula and connectivity) up to ~19 heavy atoms; or you have a set of molecular fragment-structure pairs and need to model how fragments assemble into complete structures.
    2 installs
82. ▌
    JSON Payload Construction For Nmr Spectra · holobiomicslab

    Use when when you have NMR peak assignments (1H and 13C chemical shift values) and need to submit them to the /api/smart3/search endpoint for automated structure classification. Use this skill before making API calls to ensure peak data conforms to the expected JSON schema.
    0 installs
83. ▌
    Molecular Network Clustering And Analysis · holobiomicslab

    Use when after generating candidate transformed structures from biotransformation rules and when you have MS/MS spectral feature data that you wish to organize into putative molecular families.
    0 installs
84. ▌
    Molecular Structure Prediction Evaluation · holobiomicslab

    Use when you have trained a multitask NMR-to-structure model and need to quantify its predictive accuracy on held-out test molecules.
    0 installs
85. ▌
    Molecular Structure Prediction Validation · holobiomicslab

    Use when when you have executed the MultiModalSpectralTransformer architecture on a set of multi-modal spectroscopic inputs (NMR, HSQC, COSY, IR) and obtained predicted molecular structures, and you need to assess prediction accuracy and structural correctness against ground-truth or reference.
    0 installs
86. ▌
    Nmr Metabolomic Quality Control Reporting · holobiomicslab

    Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measurements for a cohort of plasma or serum samples, and you need to assess how processing delays affect metabolite concentrations and.
    0 installs
87. ▌
    Nmr Spectrum Tiling Format Interpretation · holobiomicslab

    Use when when loading or creating an NMR spectral dataset (Dataset.createDataFile) and the system must decide between multiple storage backends (SubMatrixFile, BigMappedMatrixFile, MappedSubMatrixFile, MappedMatrixFile). Triggers include: (1) dataset metadata specifies a cache-file flag;
    0 installs
88. ▌
    Spectral Peak Data Validation And Parsing · holobiomicslab

    Use when when you have received POST requests containing peaks data as form parameters (chemical shift, multiplicity, integration values) and need to accept, validate, and normalize those values before formatting them into a query compatible with an external NMR prediction service such as.
    0 installs
89. ▌
    Structural Similarity Scoring Metabolites · holobiomicslab

    Use when when you have paired MS/MS spectra from unknown metabolites and a reference database of known metabolites, and you want to rank candidate structures for unknown compounds by their predicted structural similarity rather than exact spectral matching.
    0 installs
90. ▌
    Atac Seq Bam Read Alignment Processing · holobiomicslab

    Use when when you have aligned ATAC-seq BAM files and need to quantify Tn5 transposase insertion patterns around specific genomic coordinates (motif sites, peaks, regulatory regions) to detect transcription factor occupancy footprints or compare chromatin accessibility between bound and unbound.
    0 installs
91. ▌
    Bedgraph Format Parsing And Validation · holobiomicslab

    Use when you have generated or received bedGraph files from paired-end sequencing (via bedtools genomecov or similar) and need to verify they conform to UCSC bedGraph format before passing them to peak-calling tools like SEACR.
    0 installs
92. ▌
    Bin Level Sequencing Depth Calculation · holobiomicslab

    Use when you have a cooler file (.cool or .mcool) from a Hi-C or micro-C experiment and need to quantify the total number of sequencing reads assigned to each genomic bin to assess coverage uniformity, identify poorly-sequenced regions, or prepare bin-level weights for downstream normalization.
    0 installs
93. ▌
    Chromatin Accessibility Quantification · holobiomicslab

    Use when you have a backed AnnData object populated with fragment coordinates (stored in .obsm['fragment_paired'] or .
    0 installs
94. ▌
    Fragment Based Count Matrix Generation · holobiomicslab

    Use when you have a backed AnnData object containing processed fragment data (stored in .obsm['fragment_paired'] or .
    0 installs
95. ▌
    Hi C Normalization And Bias Correction · holobiomicslab

    Use when after generating raw Hi-C contact matrices from aligned reads (post-merge, pre-analysis).
    0 installs
96. ▌
    Hierarchical Dendrogram Interpretation · holobiomicslab

    Use when you have a methylBase object containing aligned methylation calls across multiple samples and need to verify whether samples cluster by expected experimental condition (e.g., test vs. control) or identify unexpected sample relationships.
    0 installs
97. ▌
    Iterative Lsi Dimensionality Reduction · holobiomicslab

    Use when when you have aligned paired scATAC-seq and scRNA-seq data from the same cells (multiome data) and need to create a single reduced-dimension coordinate space that integrates both chromatin accessibility and gene expression signals for joint clustering, trajectory analysis, or visualization.
    0 installs
98. ▌
    Large Scale Single Cell Matrix Loading · holobiomicslab

    Use when you have a single-cell count matrix with 10 million or more cells that must be processed through dimension reduction, clustering, or integration pipelines. Use it specifically before executing matrix-free spectral embedding (tl.
    0 installs
99. ▌
    Poisson Statistical Enrichment Testing · holobiomicslab

    Use when after extending ChIP sample reads to their predicted fragment length and constructing local lambda bias tracks (incorporating d-scaled, 1 kb, 10 kb, and genome-wide backgrounds).
    0 installs
100. ▌
     Single Cell Chromatin Sample Filtering · holobiomicslab

     Use when after loading fragment counts into a SummarizedExperiment object (e.g., via getCounts) but before motif matching or deviation computation.
     0 installs