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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   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
2. ▌
   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
3. ▌
   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
4. ▌
   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.
   2 installs
5. ▌
   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
6. ▌
   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.
   2 installs
7. ▌
   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.
   2 installs
8. ▌
   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
9. ▌
   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
10. ▌
    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
11. ▌
    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
12. ▌
    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
13. ▌
    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
14. ▌
    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
15. ▌
    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
16. ▌
    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.
    2 installs
17. ▌
    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
18. ▌
    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
19. ▌
    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
20. ▌
    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
21. ▌
    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.
    2 installs
22. ▌
    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.
    2 installs
23. ▌
    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.
    2 installs
24. ▌
    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.
    2 installs
25. ▌
    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.
    2 installs
26. ▌
    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
27. ▌
    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
28. ▌
    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
29. ▌
    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).
    2 installs
30. ▌
    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
31. ▌
    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.
    2 installs
32. ▌
    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
33. ▌
    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.
    2 installs
34. ▌
    Diversity Visualization By Treatment · holobiomicslab

    Use when you have normalized peak-abundance matrices with sample metadata containing categorical treatment variables (e.
    0 installs
35. ▌
    Docker Compose Service Orchestration · holobiomicslab

    Use when when a research software project is decomposed into distinct subproject components (e.
    0 installs
36. ▌
    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.
    2 installs
37. ▌
    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
38. ▌
    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
39. ▌
    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
40. ▌
    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.
    2 installs
41. ▌
    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
42. ▌
    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
43. ▌
    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
44. ▌
    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
45. ▌
    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
46. ▌
    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
47. ▌
    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
48. ▌
    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.
    2 installs
49. ▌
    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
50. ▌
    Organism Count Distribution Analysis · holobiomicslab

    Use when you have a flat file of structure-organism pairs (e.
    0 installs
51. ▌
    Percentile Threshold Based Filtering · holobiomicslab

    Use when you have paired genomic-metabolomic link scores (e.
    0 installs
52. ▌
    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
53. ▌
    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
54. ▌
    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
55. ▌
    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
56. ▌
    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
57. ▌
    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
58. ▌
    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
59. ▌
    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
60. ▌
    Tabular Record Filtering And Sorting · holobiomicslab

    Use when you have extracted tabular data (e.g., protocol descriptions, sample preparation steps) into an intermediate JSON representation and need to subset records by type or property (e.g., test='type=sample_prep'), then order them consistently (e.
    0 installs
61. ▌
    Tensorflow Serving Endpoint Querying · holobiomicslab

    Use when you have deployed a TensorFlow model via TensorFlow Serving in a containerized environment (e.
    0 installs
62. ▌
    Tree Structural Integrity Assessment · holobiomicslab

    Use when after generating a Chemical Feature Tree artifact (Phylogeny[Rooted]) from q2-qemistree's make-hierarchy method, or when importing a tree from external sources, to confirm it is well-formed before proceeding to alpha/beta-diversity analysis.
    0 installs
63. ▌
    Tsv CSV File Parsing And Aggregation · holobiomicslab

    Use when you have TSV or CSV files containing structure-organism pairs (with columns for structure identifier and organism identifier) and need to count unique pairs, unique structures, unique organisms, or enumerate source database identifiers to validate or report dataset scale.
    0 installs
64. ▌
    Unit Test Design For Cheminformatics · holobiomicslab

    Use when when implementing a new ComputeConverter subclass for MSMetaEnhancer that performs local chemical structure conversions using RDKit (e.g., SMILES to InChI, canonical SMILES generation).
    0 installs
65. ▌
    Unit Test Design For Data Processing · holobiomicslab

    Use when building or extending a data extraction and conversion system (such as MESSES) where tabular data is transformed via conversion directives into JSON intermediate formats and then into domain-specific schemas.
    0 installs
66. ▌
    Adduct Mass Calculation And Matching · holobiomicslab

    Use when when you have a list of target molecules with known molecular formulas and need to extract and validate their peaks from centroided mzML files, or when assessing whether detected peaks in a mass spectrometry run correspond to expected adducts of known metabolites.
    2 installs
67. ▌
    Apache Arrow Columnar Format Parsing · holobiomicslab

    Use when you have mzPeak files stored as Parquet tables within a ZIP archive and need to load spectrum metadata, chromatogram metadata, signal data (profile or centroid), or peaks into memory for analysis in R, Python, or another Arrow-supported language.
    2 installs
68. ▌
    API Error Handling And Rate Limiting · holobiomicslab

    Use when when enriching mass spectra metadata by querying multiple external web services (CIR, CTS, PubChem, IDSM, BridgeDb) asynchronously, and you need to avoid API rate-limit violations, gracefully skip missing or malformed responses, and maintain pipeline stability without losing partial.
    0 installs
69. ▌
    Appveyor Windows Build Orchestration · holobiomicslab

    Use when you are building a Qt5-based desktop application with cross-platform (macOS/Windows/Linux) distribution requirements and need to automate Windows executable generation as part of a CI/CD pipeline.
    2 installs
70. ▌
    Batch Effect Correction Combat Model · holobiomicslab

    Use when your metabolomics matrix shows evidence of systematic variation correlated with batch/run assignment (detectable via PCA separation by batch, elevated batch-dependent variance, or RLA plots showing non-zero median log-ratios).
    0 installs
71. ▌
    Batch Effect Correction Metabolomics · holobiomicslab

    Use when your metabolomics dataset exhibits samples analyzed across multiple batches or analytical runs with suspected technical drift or batch-to-batch signal shift visible as systematic separation in unsupervised clustering (PCA, hierarchical clustering).
    0 installs
72. ▌
    Biomolecule Level Pvalue Aggregation · holobiomicslab

    Use when after running iMd-ANOVA or G-test statistical analysis on normalized omics expression data with multiple biomolecules and group comparisons.
    1 install
73. ▌
    Biosynthetic Gene Cluster Annotation · holobiomicslab

    Use when when you have BGC sequences in FASTA or GenBank format and need to identify and extract biosynthetic Pfam domains for feature-based clustering, similarity search, or functional characterization.
    0 installs
74. ▌
    Black Formatter Check Mode Execution · holobiomicslab

    Use when when you need to audit whether Python source files in a repository conform to black formatting standards before accepting contributions, merging code, or running CI/CD pipelines.
    2 installs
75. ▌
    Blank Contamination Ratio Evaluation · holobiomicslab

    Use when you have a feature intensity matrix with both blank and QC (quality control) samples and need to remove features whose background contamination is too high relative to their signal in QC samples.
    0 installs
76. ▌
    Candidate Filtering And Thresholding · holobiomicslab

    Use when after generating candidate molecular formula and adduct pairs for detected m/z features, when you have observed isotopic patterns from feature detection and need to reduce annotation ambiguity by eliminating candidates with poor isotopic fit.
    2 installs
77. ▌
    Cardinal To Seurat Object Conversion · holobiomicslab

    Use when after completing Cardinal-based preprocessing (feature summarization, TIC normalization, peak processing, spatial segmentation, and SSC annotation), use this conversion when you need to leverage Seurat's downstream statistical methods—such as differential metabolite expression testing.
    2 installs
78. ▌
    Chemical Reaction Network Evaluation · holobiomicslab

    Use when you have a rule-based reaction prediction system (like Pickaxe) with a large rule set (e.g., ~1221 MetaCyc generalized rules), and you need to understand the scaling relationship between rule count and reaction coverage to decide how many rules to deploy for a specific application.
    0 installs
79. ▌
    Chemical Structure Validation Syntax · holobiomicslab

    Use when applied immediately after loading raw SMILES strings from external databases or user input during the 2_curating workflow stage, before attempting canonicalization or 2D/3D coordinate generation.
    0 installs
80. ▌
    Cloud Hosted Computational Chemistry · holobiomicslab

    Use when you have a curated dataset of ≤10,000 molecular structures with known collision cross section values for training, a target set of ≤10,000 molecules requiring CCS predictions, a compatible browser, and either lack local Python installation or prefer cloud-based execution to avoid.
    0 installs
81. ▌
    Conformer Generation And Enumeration · holobiomicslab

    Use when you have SMILES strings of molecules at specific ionization states (e.g., protonated or deprotonated adducts) and need to predict collision cross section values for mass spectrometry-based metabolite annotation.
    0 installs
82. ▌
    Container Memory Allocation Modeling · holobiomicslab

    Use when when configuring a multi-worker online deployment of a containerized Streamlit application (e.g., OpenMS workflows using RQ workers), you need to determine how many RQ worker processes can safely run in a single container given available RAM.
    2 installs
83. ▌
    Container Port Mapping Configuration · holobiomicslab

    Use when you need to deploy a containerized web application (such as MetFrag webapp on Tomcat) and make it accessible at a specific HTTP endpoint on the host machine. Use this skill when you have a Docker image with an internal service listening on a known port (e.
    0 installs
84. ▌
    Keras Model Format Conversion · holobiomicslab

    Use when you have downloaded Keras-format pre-trained models (e.g., via get_models.sh) and need to deploy them locally via TensorFlow Serving within a Dockerized classification API.
    1 install
85. ▌
    Latent Feature Interpretation · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) data preprocessed into an h5py-backed feature matrix, and a trained graph-attention autoencoder has already extracted latent low-dimensional peak features.
    2 installs
86. ▌
    Least Squares Optimization 1d · holobiomicslab

    Use when when you have a 1D signal array (e.g., extracted ion chromatogram, arrival time distribution, or MS1 spectrum intensity profile) and need to identify and quantify overlapping or adjacent peaks with precise position, height, and width estimates.
    0 installs
87. ▌
    Lipid Category Classification · holobiomicslab

    Use when a spatial metabolomics dataset contains semicolon-delimited isomer name annotations (e.g., 'all_IsomerNames' column in SpaMTP Seurat objects) and you need to collapse multiple lipid nomenclature variants into their parent lipid categories and classes.
    0 installs
88. ▌
    Lipid Set Enrichment Analysis · holobiomicslab

    Use when after completing two-group or multi-group differential expression analysis on lipidomics data when you have computed log fold-change (logFC) values and want to identify which lipid classes (e.
    0 installs
89. ▌
    Mass Spectrometry Calibration · holobiomicslab

    Use when after peak detection when you have a detected peaks table with m/z values and need to correct systematic mass drift or inaccuracy before peak alignment across multiple batches.
    0 installs
90. ▌
    Metabolite Annotation Mapping · holobiomicslab

    Use when you have a MultiAssayExperiment object with metabolite measurements (assay slot) and basic rowData (e.g., metabolite names or mass-to-charge ratios), but lack standardized chemical identifiers or pathway assignments.
    0 installs
91. ▌
    Metabolite Candidate Matching · holobiomicslab

    Use when you have: (1) a set of predicted candidate metabolites with known mass-to-charge ratios and chemical properties derived from a parent drug formula; (2) raw mass spectrometry data in mzML format from a sample suspected to contain those metabolites;
    0 installs
92. ▌
    Metabolite Formula Prediction · holobiomicslab

    Use when when you have a known drug's chemical formula and need to generate a comprehensive list of predicted metabolite formulas to match against experimental mzML mass spectrometry data.
    0 installs
93. ▌
    Metabolite Identifier Mapping · holobiomicslab

    Use when after peak detection and MS1 feature picking from merged FIA-MS spectra (typically 0–30 s acquisition window), when you have a list of accurate monoisotopic masses and need to assign HMDB compound identifiers, molecular formulas, and structural annotations to support mzTab output.
    0 installs
94. ▌
    Metabolite Similarity Scoring · holobiomicslab

    Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in .
    0 installs
95. ▌
    Metabolite To Pathway Mapping · holobiomicslab

    Use when you have a peak intensity matrix (samples × metabolites) with assigned metabolite annotations (peak ID → KEGG or ChEBI compound ID), and you need to link those identities to known metabolic pathways, molecular families, or mass2motifs before computing pathway activity scores.
    0 installs
96. ▌
    Metadata Confidence Filtering · holobiomicslab

    Use when you have curated structure-organism pairs from multiple sources and need to distinguish high-confidence, well-documented assertions from incomplete or conflicting records.
    2 installs
97. ▌
    Metadata Table Column Mapping · holobiomicslab

    Use when you have a GNPS-format TSV metadata table with mandatory columns (ATTRIBUTE_Species, ATTRIBUTE_Organe, and optional genus/family columns) and need to prepare cleaned, standardized taxonomy strings for integration into the Literature Component or cross-referencing with external reference.
    0 installs
98. ▌
    Molecular Descriptor Indexing · holobiomicslab

    Use when when you have a collection of molecular structures (SMILES or SDF format) and need to generate a queryable database of collision cross section values for high-throughput mass spectrometry workflows, or when you want to organize pre-computed CCS predictions with conformer metadata into a.
    2 installs
99. ▌
    Molecular Embedding Inference · holobiomicslab

    Use when you have a set of molecules (as SMILES strings in CSV format) and a pre-trained NaFM checkpoint, and you need to generate embeddings or predictions for virtual screening, bioactivity regression, or compound ranking tasks.
    0 installs
100. ▌
     Molecular Feature Engineering · holobiomicslab

     Use when you have a set of chemical structures (small molecules, metabolites, or drug-like compounds) represented as SMILES, SDF, mol, InChI, or mol2 files, and you need to train a machine learning model to predict a molecular property (e.g., retention time, solubility, binding affinity).
     0 installs