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HolobiomicsLab

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1. ▌
   Modification Label Normalization · holobiomicslab

   Use when when PSM files from heterogeneous proteomics search engines (MaxQuant, MSGFPlus, Sage, X!Tandem, etc.) use inconsistent or proprietary modification notations that cannot be directly consumed by feature generators (e.
   2 installs
2. ▌
   Molecular Descriptor Computation · holobiomicslab

   Use when when you have a query mass spectrum and a set of candidate molecular structures (as SMILES or 2D/3D coordinates), and you need to prepare them for cross-view similarity comparison or machine learning-based ranking.
   0 installs
3. ▌
   Molecular Structure File Parsing · holobiomicslab

   Use when when you have received or downloaded an SDF-formatted compound database file and need to verify that it is valid, uncorrupted, and contains the expected number of distinct molecular records before using it in metabolomics, cheminformatics, or toxicology workflows.
   0 installs
4. ▌
   Ms Instrument Data Preprocessing · holobiomicslab

   Use when you have raw mass spectrometry data files from a mass spectrometer instrument and need to feed them into a peptide feature detection pipeline (e.g., IsoFusion) that accepts only MS1 format input.
   0 installs
5. ▌
   Msconvert Workflow Configuration · holobiomicslab

   Use when when you need to convert vendor-specific raw mass spectrometry files (.raw) to the open mzML format using imzML Writer, and msconvert is not yet installed or its location is not recognized by the system.
   2 installs
6. ▌
   Multi Modal Projection Alignment · holobiomicslab

   Use when you have a mass spectrum and a set of candidate molecular structures, and need to rank candidates by their likelihood of matching the query spectrum.
   0 installs
7. ▌
   Multiclass Data Batch Correction · holobiomicslab

   Use when your input is a raw or prepared multi-class metabolomic peak table (in ExpressionSet format or CSV) where samples belong to distinct biological classes, and you have either QC samples (quality control replicates) or internal standards (IS) to anchor batch correction.
   0 installs
8. ▌
   Multivariate Ordination Analysis · holobiomicslab

   Use when when you have normalized peak intensities from FT-ICR MS metabolomic data (or similar high-dimensional compositional data) grouped by experimental treatments (e.g., phage type, incubation time) and want to visualize whether sample groups cluster separately in reduced dimensionality.
   2 installs
9. ▌
   Ncbi Accession Cross Referencing · holobiomicslab

   Use when you have parsed a collection of sequence files with associated GenBank/RefSeq accession identifiers (typically from JSON metadata fields like cluster.
   0 installs
10. ▌
    Neural Network Module Validation · holobiomicslab

    Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).
    0 installs
11. ▌
    Normalization Quality Assessment · holobiomicslab

    Use when after completing intra-batch and inter-batch normalisation steps on a SummarizedExperiment object containing metabolomics assays. Use it to confirm that a normalisation method (e.
    2 installs
12. ▌
    Numerical Formula Implementation · holobiomicslab

    Use when a formula is documented in a system or article (e.g., resource allocation, sizing, or tuning guidance) but lacks executable validation, or you need to confirm the formula produces the documented expected output (e.g., an 8GB system should yield exactly 4 workers).
    0 installs
13. ▌
    Omics Data Formatting Validation · holobiomicslab

    Use when when preparing raw omics data (gene expression matrices, differential abundance tables, or other quantitative omics assays) paired with sample/group metadata for import into a visualization dashboard.
    0 installs
14. ▌
    Omics Network Feature Extraction · holobiomicslab

    Use when after you have built a network object (adjacency matrix, edge list, or correlation output) from omics data and need to quantitatively describe network properties beyond visualization.
    0 installs
15. ▌
    Package Entry Point Verification · holobiomicslab

    Use when you need to confirm that a Python package (especially one distributed via pip or conda) has been correctly configured with a console script entry point and that the CLI is callable from the system shell.
    0 installs
16. ▌
    Pathway Enrichment Visualization · holobiomicslab

    Use when after running ORA on a set of significant metabolite PubChemCIDs (e.g., features with q-value < 1e-9 from ANOVA) against a metabolic pathway database, and you need to identify and communicate which pathways are robustly enriched in your case.
    2 installs
17. ▌
    Peakmap Visualization Generation · holobiomicslab

    Use when you have mass spectrometry data loaded into a Pandas DataFrame with columns for m/z, retention time (or ion mobility), and intensity, and you need to visualize the complete 2D peak map landscape to identify co-eluting features, assess data quality, or explore retention time and.
    0 installs
18. ▌
    Poisson Noise Injection Spectral · holobiomicslab

    Use when augmenting mass spectrometry ion images for contrastive learning, specifically when you need to simulate the natural Poisson noise that arises from photon-counting detectors in mass spectrometry imaging experiments.
    0 installs
19. ▌
    Polarizability Tensor Extraction · holobiomicslab

    Use when after ASE-ANI has filtered conformers to remove high-energy geometries, and you need to compute electronic properties required for CCS prediction.
    1 install
20. ▌
    Polypeptide Property Computation · holobiomicslab

    Use when you have one or more polypeptide sequences (from FASTA, CSV, or direct input) and need to compute monoisotopic mass, average mass, isotopic distribution, charge state, or isoelectric point for downstream proteomics analysis such as MS database matching, retention time prediction, or.
    0 installs
21. ▌
    Pre Analytical Variable Encoding · holobiomicslab

    Use when you have collected blood samples under specific pre-analytical conditions (known time delay before/after centrifugation in hours, processing temperature in °C, matrix type: EDTA plasma or serum) and need to query ALISTER's stability database to assess whether analyte measurements should be.
    0 installs
22. ▌
    Prima Gui Initialization Windows · holobiomicslab

    Use when you are developing a standalone Perl application for Windows that requires a graphical interface and depends on external command-line tools (e.g., Gnuplot for visualization).
    2 installs
23. ▌
    Proteomics Data Structure Design · holobiomicslab

    Use when when building a mass-spectrometry analysis pipeline that must support multiple vendor and open formats (mzML, mzXML, Thermo, Agilent, Bruker, etc.) and you need to shield downstream tools from format-specific parsing logic.
    0 installs
24. ▌
    Proteomics Output Record Parsing · holobiomicslab

    Use when after the Proteomics_Data_Processor tool has completed analysis of raw mass spectrometry files and returned structured output records.
    0 installs
25. ▌
    Pubchem Structure Lookup By Name · holobiomicslab

    Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).
    0 installs
26. ▌
    Python Package Environment Setup · holobiomicslab

    Use when when you have cloned a Python package repository and need to verify that the package installs correctly and its test suite passes locally. This is the prerequisite workflow before running pytest or code formatters like black on the package source.
    0 installs
27. ▌
    Pytorch Checkpoint Serialization · holobiomicslab

    Use when a PyTorch-based model (such as a graph neural network trained on molecular retention-time data) has completed training or reached convergence, and you need to preserve the model state for later inference, evaluation, or transfer learning on new datasets.
    0 installs
28. ▌
    Quality Control Sample Filtering · holobiomicslab

    Use when after building a SummarizedExperiment from metabolomics measurements but before batch correction and internal standard recommendation.
    0 installs
29. ▌
    Rolling Window Outlier Detection · holobiomicslab

    Use when raw LA-ICP-MS image data contains isolated spike artifacts—pixels with anomalously high or low intensities relative to their spatial neighborhood—that distort downstream quantification or visualization.
    0 installs
30. ▌
    Sample Replicate Pair Assessment · holobiomicslab

    Use when you have high-throughput replicate measurements (e.g., mass spectrometry metabolomics) on biological replicates and need to identify which sample pairs exhibit reproducible feature signals across a threshold (typically 75% reproducibility).
    0 installs
31. ▌
    Sampling Protocol Reconstruction · holobiomicslab

    Use when you have access to ALISTER's web app or codebase and need to understand, validate, or replicate the internal logic that maps (analyte, matrix, time-delay, temperature) tuples to stability assessments and protocol recommendations.
    0 installs
32. ▌
    Sequence Availability Assessment · holobiomicslab

    Use when you maintain or curate a specialized sequence repository (such as MIBiG) and need to identify which sequences in your local genbanks directory are not publicly available via NCBI GenBank/RefSeq databases.
    1 install
33. ▌
    Seurat Assay Metadata Extraction · holobiomicslab

    Use when you have a SpaMTP Seurat object with a 'Spatial' assay containing metabolomics features (m/z values) and their associated metadata columns (e.
    0 installs
34. ▌
    Spatial Metabolomics Integration · holobiomicslab

    Use when when you have paired spatial metabolomics and spatial transcriptomics measurements from the same tissue samples and need to identify how metabolite distributions relate to gene expression patterns at aligned spatial coordinates.
    0 installs
35. ▌
    Spectral Data Integrity Checking · holobiomicslab

    Use when after converting mass-spectrometry data from an existing format (mzML, mzXML, or vendor-specific formats) into mzPeak using command-line tools or API calls.
    1 install
36. ▌
    Spot Level Intensity Aggregation · holobiomicslab

    Use when after loading spatial metabolomics data (from CSV, imzML, or merged positive/negative ion modes) into an AnnData object, and before filtering or alignment steps.
    0 installs
37. ▌
    Sra Data Retrieval And Ingestion · holobiomicslab

    Use when your analysis requires raw sequencing reads stored in NCBI SRA (identified by SRR, SRX, or SRP accessions) OR you have local FASTQ files organized in a directory structure.
    0 installs
38. ▌
    Statistical Significance Testing · holobiomicslab

    Use when when you have computed rank-based accuracy metrics (top-1, top-5, top-10 hit rates) for two or more competing methods on the same test dataset (e.g., Orbitrap spectra), and need to determine whether performance differences are genuine rather than noise.
    2 installs
39. ▌
    Statistical Simulation Execution · holobiomicslab

    Use when you have access to a published repository containing simulation scripts (e.
    0 installs
40. ▌
    Structure File Format Conversion · holobiomicslab

    Use when you have raw structure input from diverse external databases (e.
    2 installs
41. ▌
    Taxonomic Classification Merging · holobiomicslab

    Use when you have a GNPS DBResult file with spectral library matches that lack ClassyFire superclass, class, and subclass annotations, and you need to augment those matches with standardized chemical taxonomy for consensus classification or downstream analysis.
    0 installs
42. ▌
    Test Driven Database Development · holobiomicslab

    Use when when you have an existing tool or library with file-based storage (JSON, CSV, binary formats) that needs to support efficient querying across large datasets, and you want to migrate to a relational database without breaking existing functionality or performance expectations.
    0 installs
43. ▌
    Total Ion Current Quantification · holobiomicslab

    Use when you have loaded a mass spectrometry imaging pixel array (NumPy format) and need to correct for variations in total ion signal across pixels before generating ion images or ratio images.
    0 installs
44. ▌
    Variational Autoencoder Training · holobiomicslab

    Use when after preprocessing and normalizing joint ST/SM AnnData objects using joint_adata_sm_st and normalize_total_joint_adata_sm_st, when you need to align spatial transcriptomics and metabolomics data to a unified latent resolution for multi-omics integration and cross-modal spatial pattern.
    0 installs
45. ▌
    Visual Studio Project Management · holobiomicslab

    Use when when you have cloned a multi-framework .NET project (e.g., MsdialWorkbench using .NET Framework 4.7.2, .NET Core 3.1, and .NET 6) and need to set up the build environment in Visual Studio, restore dependencies, select a specific build configuration (e.
    2 installs
46. ▌
    Masst Repository Scale Search Workflow · holobiomicslab bundle

    Use when you have a spectrum or feature of interest and want to know where else it occurs across all public metabolomics data — query preparation, repository-scale fastMASST search, specialized microbe/plant/food MASST for ecological context, and co-occurrence analysis.
    0 installs
47. ▌
    Ms2lda Substructure Discovery Workflow · holobiomicslab bundle

    Use when you want to discover shared substructures (Mass2Motifs) across a corpus of MS2 spectra via LDA topic modeling — convert MS/MS spectra into a bag-of-fragments document corpus, run MS2LDA (Latent Dirichlet Allocation) to infer recurring fragmentation motifs, annotate motifs against MotifDB / Spec2Vec embeddings, and map motifs back onto molecular-network features for substructure-level annotation of an untargeted LC-MS/MS dataset.
    0 installs
48. ▌
    Isoform Usage Bias Correction · holobiomicslab

    Use when when performing gene-level differential expression analysis on RNA-seq data where samples may express different isoforms of the same gene at different relative abundances. Specifically: (1) you have transcript-level quantification (e.
    2 installs
49. ▌
    Matrix Equivalence Validation · holobiomicslab

    Use when you have generated gene-level count matrices via two methodologically distinct routes—e.
    0 installs
50. ▌
    Quantification Output Parsing · holobiomicslab

    Use when you have transcript-level quantification output files (e.g., quant.sf from salmon, abundance.
    0 installs
51. ▌
    Read Mapping Rate Calculation · holobiomicslab

    Use when when comparing mapping performance between two mapper implementations (e.g., C++ salmon vs. Rust salmon), validating that a bug fix or algorithmic change did not degrade sensitivity, or establishing baseline quantification quality on benchmark datasets with known characteristics.
    0 installs
52. ▌
    Sparse Matrix Format Handling · holobiomicslab

    Use when your input is an AnnData object with expression matrix X as a sparse scipy matrix or Dask-backed array, and you need to apply preprocessing functions (normalization, PCA, filtering) that could trigger eager materialization.
    0 installs
53. ▌
    Spatial Omics Dataset Loading · holobiomicslab

    Use when you have a spatial transcriptomics experiment (e.
    0 installs
54. ▌
    Splicing Matrix Normalization · holobiomicslab

    Use when you have transcript-level quantification (TPM or counts from Salmon/kallisto) and need to quantify the inclusion level of specific alternative splicing events (exon skipping, intron retention, alternative splice sites, etc.) in a form suitable for differential splicing analysis across.
    0 installs
55. ▌
    Biomolecular Class Label Assignment · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or databases).
    0 installs
56. ▌
    Breath Sample Feature Normalization · holobiomicslab

    Use when after peak recognition has identified significant m/z signals in individual breath samples and you need to aggregate features by sample identifier before aligning features across multiple samples.
    2 installs
57. ▌
    High Dimensional Signal Enhancement · holobiomicslab

    Use when when you have raw or preprocessed mass spectrometry imaging (MSI) data with limited spatial resolution, high noise, or incomplete molecular coverage, and you want to enhance signal fidelity to support multiscale tissue–single-cell mapping or brain biochemical profiling.
    0 installs
58. ▌
    Metabolite Library Entry Generation · holobiomicslab

    Use when you have an experimental MS/MS spectrum (from MassBank or your own acquisition) and need to create a standardized library entry with ranked fragment ions for use in MetaboAnnotatoR or other fragment-based annotation pipelines.
    0 installs
59. ▌
    Ms1 Composite Spectra Deconvolution · holobiomicslab

    Use when you have high-resolution MS1 data (mzXML, mzML, or netCDF format) from LC/HRMS analysis and need to deconvolve composite spectra into individual fragmentation patterns without DDA or DIA acquisition.
    0 installs
60. ▌
    Msp File Parsing Edge Case Handling · holobiomicslab

    Use when you are parsing mass spectrometry spectral library files in MSP format and need to guarantee that all spectrum records are either successfully integrated into the final dataset or explicitly logged with a reason for exclusion.
    0 installs
61. ▌
    Numeric Array Round Trip Validation · holobiomicslab

    Use when after implementing or modifying a numerical compression codec (such as MSNumpressCoder for m/z and intensity arrays in mass-spectrometry workflows) to verify that round-trip encode–decode cycles preserve numerical values within expected tolerance.
    2 installs
62. ▌
    Sample Information Metadata Parsing · holobiomicslab

    Use when when you have a validated ReDU sample-information metadata file (gnps_metadata.
    0 installs
63. ▌
    Adduct Ionmode Consistency Checking · holobiomicslab

    Use when parsing, standardizing, or filtering MS spectra from mixed or heterogeneous databases where adduct assignment may be manually entered, auto-inferred, or missing.
    0 installs
64. ▌
    Chemical Match Score Interpretation · holobiomicslab

    Use when when you have query chemicals identified by GC-MS (with Match.Factor values) and need to verify structural similarity against a reference chemical library to confirm compound identity or detect structural analogs (e.g., isomers or homologs).
    0 installs
65. ▌
    Compound Identifier Standardization · holobiomicslab

    Use when ingesting compound metadata from multiple sources (PubChem, DrugBank, LOTUS, Dictionary of Natural Products, DrugCentral) that lack uniform column naming, have incomplete structure information, or contain only compound names without structural data.
    0 installs
66. ▌
    Eic Similarity Correlation Analysis · holobiomicslab

    Use when after abundance-correlation-based feature group refinement when you observe that larger feature groups (particularly those with 3+ features in the same m/z–retention-time window) may contain features with different peak shapes or retention-time shifts in their EICs, or when abundance.
    0 installs
67. ▌
    File Path Resolution And Validation · holobiomicslab

    Use when when initializing a SmartPeak session from a sequence file, you need to load and validate the workflow.csv and sequence.csv files that are co-located in the session directory.
    0 installs
68. ▌
    Fragmentation Database Construction · holobiomicslab

    Use when when you have completed ORCA single-point energy calculations on interpolated reaction pathway geometries and need to convert quantum mechanical fragment energies and molecular properties into a structured fragmentation channel database suitable for automated EI mass spectrum simulation.
    0 installs
69. ▌
    Gc Ms Molecular Family Organization · holobiomicslab

    Use when after auto-deconvolution of GC-MS data has produced a table of individual deconvolved mass spectra (one per detected peak), and your goal is to group spectra into molecular families based on mass spectral similarity rather than retention time or chemical class.
    2 installs
70. ▌
    Library Spectrum Database Searching · holobiomicslab

    Use when you have an unknown electron ionization (EI) mass spectrum and need to identify the compound by comparing it against a reference library (msp file format).
    0 installs
71. ▌
    Mass Spectrometry Raw Data Encoding · holobiomicslab

    Use when you have generated or obtained a two-dimensional mass-spectrometry intensity matrix (m/z × retention time scan points) with simulated or experimental peak shapes, noise, and background, and need to encode it as a binary .
    0 installs
72. ▌
    Metabolomic Feature Table Filtering · holobiomicslab

    Use when after feature detection (e.g., Asari processing of mzML files to feature tables) but before normalization, batch correction, or annotation.
    0 installs
73. ▌
    Metabolomics Feature Table Curation · holobiomicslab

    Use when you have a raw feature table (TSV/CSV) derived from LC-MS peak detection (e.
    0 installs
74. ▌
    Metabolomics Feature Transformation · holobiomicslab

    Use when when you have a feature intensity table (samples × compounds) from targeted or non-targeted metabolomics and need to prepare it for statistical modeling or multivariate analysis.
    0 installs
75. ▌
    Orthogonal Projection Deconvolution · holobiomicslab

    Use when you have overlapped peak regions in GC-MS chromatography data (multiple components eluting within the same retention time window) and need to recover the pure mass spectra of each component and their relative concentrations.
    0 installs
76. ▌
    Rank Performance Metric Computation · holobiomicslab

    Use when when you have predictions from one or more metabolite annotation models (MLP baseline, GNN, or ESP ensemble) and need to quantify ranking performance on ESI/LC-MS test spectra.
    0 installs
77. ▌
    Spectral Match Score Interpretation · holobiomicslab

    Use when when you have GC-MS output with Match.Factor values or structural similarity scores from categorate() and need to decide which identified compounds are reliable enough to carry forward. Specifically: (1) after running GC-MS and receiving a Match.Factor column;
    0 installs
78. ▌
    Two Dimensional Ms Image Processing · holobiomicslab

    Use when you have raw GC–MS or LC–MS data represented as a two-dimensional map (m/z axis vs. retention time axis) and need to identify chemo-/biomarker features across multiple analytes simultaneously, especially when conventional peak picking produces high false-positive or false-negative rates.
    0 installs
79. ▌
    Whittaker Smoother Signal Denoising · holobiomicslab

    Use when after baseline correction (e.g., via asymmetric least squares) when raw GCxGC-MS chromatograms still contain high-frequency noise that obscures true signal structure. Use it when you need to reduce noise before peak alignment or multivariate analysis (e.
    0 installs
80. ▌
    Acquisition Method Overlap Analysis · holobiomicslab

    Use when you have acquired the same sample(s) using multiple LC-MS, LC-IMS-MS, or direct infusion methods (e.
    0 installs
81. ▌
    Adduct Ion Prediction And Filtering · holobiomicslab

    Use when when annotating m/z features against a metabolite database (HMDB, Lipidmaps, etc.) and the sample preparation, ionization method, or polarity mode favors specific adduct species. For example: negative-mode LC-MS or MS imaging will preferentially generate M-H and halide adducts (M+Cl);
    0 installs
82. ▌
    Adduct Mass Matching And Clustering · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.g. via MB-VIP permutation testing) when you need to consolidate redundant measurements of the same metabolite arising from different ionisation adducts (e.g. [M+H]+, [M+Na]+, [M−H]−).
    0 installs
83. ▌
    Adduct Mass Offset Parameterization · holobiomicslab

    Use when when processing LC-MS metabolomics feature tables where adduct annotation is absent or incomplete, and you need to identify which ionization adducts are present in your mass spectrometry data.
    0 installs
84. ▌
    Mass Spectrometry Data Visualization · holobiomicslab

    Use when after applying retention time, abundance correlation, or EIC similarity-based feature grouping (e.g., via SimilarRtimeParam, AbundanceSimilarityParam, or EicSimilarityParam). Use when you need to visually confirm that grouped features belong to the same compound—i.
    0 installs
85. ▌
    Mass Spectrometry Feature Annotation · holobiomicslab

    Use when when you have peak-detected LC-MS/MS data (MGF files with MS1 and MS2 spectra, plus a feature abundance table from MZmine2) and need to assign chemical structures and molecular properties to individual MS1 features rather than relying on mass-to-charge alone.
    0 installs
86. ▌
    Mass Spectrometry Feature Clustering · holobiomicslab

    Use when after XCMS feature detection and alignment when you have a CSV-formatted feature table with m/z and retention time annotations and want to deduplicate isotopic peaks, adducts, and in-source fragments into compound-level clusters before molecular weight inference or spectral matching.
    0 installs
87. ▌
    Mass Spectrometry Metric Engineering · holobiomicslab

    Use when you have raw DIA mass spectrometry files (.raw, .d, .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to quantify file quality for automated quality control, longitudinal instrument monitoring, or training a quality prediction classifier.
    0 installs
88. ▌
    Mass Spectrometry Spectral Alignment · holobiomicslab

    Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally modified variant of that compound—and you need to identify which atoms in the structure likely bear the modification.
    0 installs
89. ▌
    Mass Tolerance Calibration Ppm Units · holobiomicslab

    Use when when linking statistically significant LC-MS features into structural clusters based on adduct signatures and cross-assay references (e.g., [M+H]+/[M-H]−), and you need to specify the maximum allowed deviation (in ppm) between observed m/z values and calculated neutral masses.
    2 installs
90. ▌
    Massgrid Construction And Validation · holobiomicslab

    Use when after individual mass tracks (EICs) have been extracted from each sample's mzML file and you need to create a unified, cross-sample m/z reference structure. Triggered when: (1) you have ≥2 samples in a cohort; (2) mass tracks have been binned at 0.
    0 installs
91. ▌
    Maximum Weight Matching Optimization · holobiomicslab

    Use when you have computed pairwise similarity or mass difference scores between all fragment ions across two tandem mass spectra and need to select the non-overlapping set of ion pair matches.
    0 installs
92. ▌
    Metabolite Database Embedding Lookup · holobiomicslab

    Use when when you have paired tandem MS spectra and known molecular structures (SMILES or fingerprints) and want to annotate novel spectra by retrieving similar structures from a reference database without relying on spectral database matching.
    0 installs
93. ▌
    Metabolite Network Format Conversion · holobiomicslab

    Use when after downloading GNPS molecular networking results (from GNPS1 or GNPS2 workflows), use this skill to extract and standardize the compressed archive into named, canonicalized files (spectra.mgf, molecular_families.tsv, annotations.tsv, file_mappings.tsv/.
    0 installs
94. ▌
    Metabolite Quality Control Filtering · holobiomicslab

    Use when after feature extraction (Asari) has produced a full feature table from mzML data, but before normalization and annotation.
    0 installs
95. ▌
    Metabolite Quality Metric Assessment · holobiomicslab

    Use when after drift correction has been applied to a MetaboSet object, and before imputation and batch correction.
    0 installs
96. ▌
    Metabolite Stoichiometry Computation · holobiomicslab

    Use when when you have quantified intracellular metabolite abundances (LC-MS normalized values) for multiple cell lines or samples, a metabolic network model with reaction stoichiometry, and you need to predict how substrate availability translates into metabolic flux differences.
    0 installs
97. ▌
    Metabolomic Feature Table Imputation · holobiomicslab

    Use when after feature detection and peak alignment have produced a feature table with zero or missing values across samples.
    0 installs
98. ▌
    Metabolomics Data Quality Assessment · holobiomicslab

    Use when after consolidating aligned LC-MS peaks into a quantitative feature table (with m/z, retention time, and intensity values across all samples), and before proceeding to statistical analysis or functional interpretation.
    0 installs
99. ▌
    Metabolomics Feature Table Filtering · holobiomicslab

    Use when when you have a raw LC-MS peak table imported from vendor software (e.
    1 install
100. ▌
     Metabolomics Intensity Normalization · holobiomicslab

     Use when your input is a raw metabolomics intensity matrix (compounds × samples) with known batch assignment and QC sample labels, and you observe signal drift across the analytical sequence or batch-to-batch variation.
     0 installs