← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 7.4k skills
• 0 followers
• 2 days ago last updated

1. ▌
   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
2. ▌
   Tensorflow Serving Endpoint Querying · holobiomicslab

   Use when you have deployed a TensorFlow model via TensorFlow Serving in a containerized environment (e.
   0 installs
3. ▌
   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
4. ▌
   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
5. ▌
   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
6. ▌
   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
7. ▌
   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.
   0 installs
8. ▌
   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.
   0 installs
9. ▌
   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
10. ▌
    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.
    0 installs
11. ▌
    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
12. ▌
    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
13. ▌
    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.
    0 installs
14. ▌
    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
15. ▌
    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.
    0 installs
16. ▌
    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
17. ▌
    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.
    0 installs
18. ▌
    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.
    0 installs
19. ▌
    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
20. ▌
    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
21. ▌
    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
22. ▌
    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
23. ▌
    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.
    0 installs
24. ▌
    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
25. ▌
    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.
    0 installs
26. ▌
    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.
    0 installs
27. ▌
    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
28. ▌
    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
29. ▌
    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
30. ▌
    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
31. ▌
    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
32. ▌
    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
33. ▌
    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
34. ▌
    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
35. ▌
    Metabolite Similarity Scoring · holobiomicslab

    Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in .
    0 installs
36. ▌
    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
37. ▌
    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.
    0 installs
38. ▌
    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
39. ▌
    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.
    0 installs
40. ▌
    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
41. ▌
    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
42. ▌
    Molecular Structure Alignment · holobiomicslab

    Use when when you have two or more lipid structures represented as labeled molecular graphs and need to compute pairwise structural distances to cluster lipidomes, identify similar lipid species, or rank lipids by structural relatedness.
    0 installs
43. ▌
    Msi Peak Intensity Extraction · holobiomicslab

    Use when you have MSI intensity data exported from commercial software (MSiReader, SCiLS) or Cardinal processing pipelines as plain-text CSV files or Cardinal MSProcessedImagingExperiment/MSContinuousImagingExperiment objects, and you need to prepare it for mass-difference tabulation and adduct.
    0 installs
44. ▌
    Network Topology Edge Parsing · holobiomicslab

    Use when you have a metabolic or biological network encoded as pairwise directed interactions (e.
    0 installs
45. ▌
    Parameter Tuning Metabolomics · holobiomicslab

    Use when you have at least 3 raw mass spectrometry samples in open formats (mzML, mzXML, CDF) from untargeted metabolomics experiments and need to configure parameters for XCMS, MZmine2, or similar processing software.
    0 installs
46. ▌
    Peak Border Center Estimation · holobiomicslab

    Use when you have LC-HRMS chromatograms in retention time × m/z matrix format and need to automatically localize chromatographic peak positions and extents prior to matching against a reference peak library or generating CNN training instances.
    0 installs
47. ▌
    Per Lipid Class Normalization · holobiomicslab

    Use when you have IM-MS lipidomic data from samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract), measured CCS values stratified by lipid class and adduct type, and access to the DTCCS_N2 reference library for U13C lipids.
    0 installs
48. ▌
    Per Root Metabolite Profiling · holobiomicslab

    Use when when you have deposited mass spectrometry imaging datasets for plant roots in CDF format paired with pre-computed Matlab workspaces, and you need to reproduce per-root linear-axis metabolite profiling outputs to validate reported genotype-level results (e.
    0 installs
49. ▌
    Pip Package Manager Operation · holobiomicslab

    Use when when you have cloned or downloaded a Python project repository and need to install all declared dependencies to make the package importable and functional. Use this skill at the start of any local setup workflow when a requirements.
    0 installs
50. ▌
    Preference System Integration · holobiomicslab

    Use when when a GUI widget (e.g., isotopes display, compound list, or analysis parameter panel) must show or hide content according to user selections stored in application preferences, and the current implementation either shows all content regardless of preference or lacks a preference-reading.
    0 installs
51. ▌
    Pseudo Data Pair Construction · holobiomicslab

    Use when when you have a raw list of SMILES strings but lack sufficient real mass spectrometry reference data (typically <300 spectra) to train a generative model for unknown chemical identification.
    0 installs
52. ▌
    Psm Score Sorting And Ranking · holobiomicslab

    Use when when you have grouped PSMs by spectrum identifier and need to (1) establish input candidate PSMs for rescoring by selecting top-ranked PSMs based on search engine score, or (2) re-rank PSMs after rescoring completes to select final output PSMs for FDR calculation and result writing.
    0 installs
53. ▌
    Query Language Grammar Design · holobiomicslab

    Use when when you need to enable non-programmer mass spectrometry users to express complex spectral search patterns (e.g., isotope patterns, precursor mass constraints, scan-type filters) without writing procedural code.
    0 installs
54. ▌
    R Bioconductor Omics Workflow · holobiomicslab

    Use when you have a raw or partially processed multi-class or time-series metabolomic peak table (in standardized or software-specific format) and need to determine which combination of imputation, QC sample normalization, transformation, and metabolite/sample-based normalization methods will.
    0 installs
55. ▌
    R Function Workflow Execution · holobiomicslab

    Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE barocycler-based concurrent multiomics method and need to perform integrative preprocessing (spectral normalization and alignment across samples) followed by multivariate analysis to identify differential lipids.
    0 installs
56. ▌
    Random Walk Graph Propagation · holobiomicslab

    Use when you have: (1) a set of spectral library matches (seed identities) mapped to molecular structures, (2) a candidate structure graph derived from in silico fragmentation (e.
    0 installs
57. ▌
    Resource Capacity Calculation · holobiomicslab

    Use when when configuring an OpenMS Streamlit application for online deployment with Redis and RQ worker processes, you need to determine how many worker processes can safely run in parallel within a Docker container's memory constraint.
    0 installs
58. ▌
    Robust Regression Gam Fitting · holobiomicslab

    Use when metabolomics intensity data exhibits systematic signal drift across sample runs (especially within batches), QC samples are available to anchor normalization, and you require robustness against outlier compounds or aberrant sample intensities.
    0 installs
59. ▌
    Roi Definition And Extraction · holobiomicslab

    Use when when you have loaded imzML MSI data into napari and need to focus analysis on a specific anatomical or morphological region rather than the entire image.
    0 installs
60. ▌
    Run Order Diagnostic Plotting · holobiomicslab

    Use when you have metabolomics data structured as a SummarizedExperiment with run-order metadata and need to diagnose whether signal intensity or abundance varies systematically with sample acquisition order (intra-batch drift) or batch assignment (inter-batch effects).
    0 installs
61. ▌
    Sample Matrix Effect Handling · holobiomicslab

    Use when you have measured metabolites or lipids from archival blood samples (e.
    0 installs
62. ▌
    Saturated Peak Reconstruction · holobiomicslab

    Use when processing IM-MS data files (Agilent .d or UIMF format) that contain high-abundance ions suspected of signal saturation, particularly in untargeted or discovery proteomics/metabolomics workflows where dynamic range compression would obscure quantitative relationships.
    0 installs
63. ▌
    Scan Filter File Organization · holobiomicslab

    Use when when converting mzML files to imzML format and the source mzML contains multiple scan filters (e.g., different MS/MS isolation windows, ionization modes, or mass ranges acquired in a single imaging experiment).
    0 installs
64. ▌
    Sirius Zodiac Score Filtering · holobiomicslab

    Use when after running SIRIUS on a mass spectrometry feature set and obtaining compound_identification.tsv output containing Zodiac and Cosmic confidence scores, apply this filter to eliminate low-confidence SIRIUS annotations before downstream prioritization or chemical class analysis.
    0 installs
65. ▌
    Slurm Gpu Resource Allocation · holobiomicslab

    Use when you have a machine learning training workflow (e.g., k-fold cross-validation) where each fold is independent, can run in parallel, and requires exactly one GPU per fold.
    0 installs
66. ▌
    Smarts Reaction Rule Encoding · holobiomicslab

    Use when when you have a set of known chemical reactions (e.g., from MetaCyc or KEGG) that you want to generalize into reusable transformation rules for predicting novel reactions on new compound sets.
    0 installs
67. ▌
    Species Identifier Annotation · holobiomicslab

    Use when you have a parsed lipid species table output from LipidSearch or LIQUID containing lipid names or identifiers and their quantitative measurements, but lack standardized taxonomic annotation (e.g., Glycerophospholipids, Phosphatidylcholines).
    0 installs
68. ▌
    Spectral Database Compilation · holobiomicslab

    Use when you have generated predicted fragment spectra for a set of compounds using CFM-ID or similar in-silico prediction tools and need to organize these results into a persistent, queryable database that mirrors the schema of an existing online spectral reference (such as the predicted-fragments.
    2 installs
69. ▌
    Spectral Peak Data Extraction · holobiomicslab

    Use when when you need to retrieve m/z–intensity pairs from a MsBackend-backed Spectra object for visualization, comparison, or processing; particularly when the backend stores peak data separately (e.
    0 installs
70. ▌
    Spectral Peak Feature Hashing · holobiomicslab

    Use when when you have a large collection of query high-resolution mass spectra that must be rapidly matched against a spectral library containing modified and unmodified peptides, and you need to reduce computational overhead before approximate nearest neighbor indexing or GPU-accelerated.
    0 installs
71. ▌
    Spectrum Object Instantiation · holobiomicslab

    Use when after successfully parsing raw spectral data from one of the supported file formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) into intermediate dictionaries containing m/z arrays, intensity arrays, and metadata key-value pairs.
    0 installs
72. ▌
    Spectrum Object Schema Design · holobiomicslab

    Use when when building a mass spectrometry data import pipeline that must ingest spectra from multiple file formats and produce a unified, queryable representation suitable for metadata validation, peak filtering, and similarity comparisons.
    0 installs
73. ▌
    Spectrum Tokenization For Nlp · holobiomicslab

    Use when when you have raw mass spectra from experimental libraries (e.
    0 installs
74. ▌
    Structured Data Serialization · holobiomicslab

    Use when when you have mwTab-formatted Mass Spectrometry or Nuclear Magnetic Resonance experimental data from the Metabolomics Workbench that must be converted to JSON for API integration, data sharing across systems, or validation against a defined JSON schema.
    0 installs
75. ▌
    Study Size Weighted Averaging · holobiomicslab

    Use when you have metabolomics results from multiple independent studies (each with a fold-change, p-value, and sample size N) and need to produce a single quantitative meta-analysis fold-change estimate.
    0 installs
76. ▌
    Tensorflow Hdf5 Serialization · holobiomicslab

    Use when when you have acquired Keras models (via get_models.sh or similar download) and need to deploy them locally through TensorFlow Serving within a Docker/docker-compose stack.
    0 installs
77. ▌
    Tensorflow Serving Deployment · holobiomicslab

    Use when you have trained Keras models that need to be served as microservices for real-time inference. Specifically: (1) models have been converted to HDF5 TensorFlow 2.3.0 format with properly named input layers ('input_2048', 'input_4096') and output layer ('output');
    0 installs
78. ▌
    Tic Peak Isolation Validation · holobiomicslab

    Use when you have raw mass spectrometry data (mzML, mzXML, or CDF format) from at least 3 samples and need to automatically identify candidate peak regions in the TIC chromatogram before extracting ion-level parameters for XCMS or MZmine2 processing.
    0 installs
79. ▌
    Workflow Context Preservation · holobiomicslab

    Use when when submitting OpenMS workflows to RQ (Redis Queue) in online Docker mode, you need to preserve the job ID and execution context for recovery after container restarts or worker failures. Apply this skill if: (1) you are using QueueManager.
    0 installs
80. ▌
    Ion Mobility 4d Annotation Workflow · holobiomicslab bundle

    Use when you have ion-mobility LC-IMS-MS/MS data (e.g. timsTOF / PASEF) and want CCS-aware annotations — 4D feature extraction with collision cross section, CCS calibration and filtering, CCS-aware library matching, and (optional) networking.
    0 installs
81. ▌
    Lipidomics Lcms Annotation Workflow · holobiomicslab bundle

    Use when you have untargeted lipidomics LC-MS/MS data (mzML) and want a class- and species-level annotated lipid feature table — preprocessing, normalization, lipid identification by MS/MS, retention/adduct rule validation, differential analysis, and a fused master table.
    0 installs
82. ▌
    Nmr Metabolomics Profiling Workflow · holobiomicslab bundle

    Use when you have NMR metabolomics data (1D/2D spectra or FIDs) and want a quantified, identified metabolite profile — spectral preprocessing (phase/baseline/referencing, binning), metabolite identification by chemical shift, quantification, and group statistics.
    0 installs
83. ▌
    Leiden Clustering Of Cells · holobiomicslab

    Use when after constructing a kNN graph (via pp.neighbors) on preprocessed, scaled, and PCA-reduced single-cell expression data.
    0 installs
84. ▌
    Transcript To Gene Mapping · holobiomicslab

    Use when you have transcript-level quantification files (salmon quant.sf.gz, kallisto, or Sailfish output) and need to perform gene-level differential expression analysis.
    0 installs
85. ▌
    Ce Ms Migration Time Measurement · holobiomicslab

    Use when when processing raw CE-MS data and need to establish a baseline migration time scale before transforming to effective mobility.
    0 installs
86. ▌
    Mass Spectrum Peak Normalization · holobiomicslab

    Use when when comparing two or more MSMS spectra using intensity-weighted similarity measures (cosine similarity, modified cosine, or neutral loss similarity), and the spectra have been acquired under different instrumental conditions, ionization efficiencies, or detector gains that produce.
    0 installs
87. ▌
    Model Inference And Tokenization · holobiomicslab

    Use when you have MS/MS spectra in .msp format and need to retrieve similar compounds or compute spectral similarities for compound identification. The input spectra should already be cleaned (malformed or invalid SMILES removed), and you have access to a pre-trained SpecEmbedding model checkpoint.
    0 installs
88. ▌
    Molecular Similarity Calculation · holobiomicslab

    Use when you have two or more molecular structures (represented as SMILES or spectral data) and need to rank transformation product candidates by structural plausibility, filter isomeric or duplicate TP predictions, or group features into components based on chemical relatedness.
    0 installs
89. ▌
    Singularity Container Deployment · holobiomicslab

    Use when you have a Nextflow workflow (e.g., Nextflow4MS-DIAL) that currently runs under Docker or bare metal, and you need to execute it on an HPC cluster that lacks Docker support or enforces Singularity as the container runtime.
    0 installs
90. ▌
    Batch Effect Matrix Construction · holobiomicslab

    Use when when you need to generate synthetic metabolomics feature tables with quantified batch effects for validating batch-correction methods. Use this skill when: (1) you want reproducible, ground-truth batch effects overlaid on condition-only variation;
    0 installs
91. ▌
    Chemical Identifier Verification · holobiomicslab

    Use when when you have a list of chemically known compounds and need to validate that an MS processing pipeline (e.g., mzExacto) correctly retrieves their characteristic m/z, retention time, match factor, and area values from GC-MS data.
    0 installs
92. ▌
    Chemical Mass Tolerance Matching · holobiomicslab

    Use when when you have a metabolomics peak list (m/z values with optional retention times) from LC-MS or GC-MS and want to filter a computationally expanded chemical library to only compounds whose calculated masses (accounting for ionization adducts) fall within a defined tolerance of observed.
    0 installs
93. ▌
    Fticr Mass Calibration Edgeshift · holobiomicslab

    Use when you have FTICR-MS direct injection (mzML) data with identified chromatographic peaks and need to correct systematic m/z bias.
    0 installs
94. ▌
    Gc Ims Peak Alignment Evaluation · holobiomicslab

    Use when after peak detection in GC-IMS preprocessing, when you need to assess whether detected peaks from multiple samples align to the same chemical entities (clusters) using hierarchical clustering.
    0 installs
95. ▌
    Gcxgc Preprocessed Data Handling · holobiomicslab

    Use when you have preprocessed individual GCxGC-MS chromatograms (each smoothed with Whittaker smoother, baseline-corrected with asymmetric least squares, and aligned against a reference using 2D correlation optimized warping) and need to consolidate them into a single analytical object for.
    0 installs
96. ▌
    Ion Mobility Dimension Detection · holobiomicslab

    Use when when processing raw mass spectrometry data files of unknown or mixed provenance, and you need to automatically route IMS inputs to their corresponding analysis pipeline.
    0 installs
97. ▌
    Log Transformation Preprocessing · holobiomicslab

    Use when apply log transformation when peak intensity distributions are right-skewed with heteroscedastic variance (intensity-dependent noise), particularly in QC-based batch correction workflows where variance stabilization improves the effectiveness of subsequent Pareto scaling normalization.
    0 installs
98. ▌
    Mass Spectrometry Data Alignment · holobiomicslab

    Use when you have two LC-MS feature tables (each containing m/z, retention time, and intensity columns) from the same or related biological samples and need to identify which features in dataset A correspond to which features in dataset B.
    0 installs
99. ▌
    Mass Spectrum Peak List Handling · holobiomicslab

    Use when you have raw or preprocessed electron ionization (EI) mass spectral data that must be stored in, retrieved from, or validated against the MSP file format (used by NIST MS Search and similar spectral library tools).
    0 installs
100. ▌
     Match Factor Threshold Filtering · holobiomicslab

     Use when you have a GC-MS dataset with Match.Factor scores for each detected compound (output from Agilent Unknowns Analysis or equivalent), and you want to reduce the number of query chemicals passed to computationally intensive cheminformatics functions (categorate, mzExacto, or exactoThese).
     0 installs