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HolobiomicsLab

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1. ▌
   Poisson Test Statistical Scoring · holobiomicslab

   Use when after generating ChIP pileup and local lambda (background) BEDGRAPH tracks with matched sequencing depth, use this skill to assign statistical significance scores to each genomic region.
   0 installs
2. ▌
   Probe Detection Pvalue Filtering · holobiomicslab

   Use when immediately after loading raw methylation array data (.idat files or beta-valued matrix) from HumanMethylation450 (450k) or EPIC arrays when conducting primary quality control.
   0 installs
3. ▌
   Random Matrix Theory Application · holobiomicslab

   Use when when analyzing normalized DNA methylation beta matrices (450K or EPIC arrays) and you need to identify the true number of latent batch or technical factors present in the data.
   0 installs
4. ▌
   Adduct Mass Difference Matching · holobiomicslab

   Use when you have computed a histogram of pairwise mass differences from MS imaging data and need to (1) identify which observed mass differences correspond to biologically relevant or chemically known adducts, or (2) rank the most frequently observed mass differences to discover dominant adduct.
   0 installs
5. ▌
   Batch Corrected Data Extraction · holobiomicslab

   Use when after batch correction has been applied to metabolomics data using pooled SQC samples, and you need to retrieve the corrected ratios (compound / internal standard) for quality metrics calculation, internal standard recommendation, concentration estimation, or statistical modelling.
   0 installs
6. ▌
   Biclustering For Omics Features · holobiomicslab

   Use when you have a normalized matrix of feature attribution scores (microbes × metabolites) derived from a trained neural network, and you want to partition both microbes and metabolites simultaneously into co-clusters that share similar interaction patterns.
   0 installs
7. ▌
   Biotransformation Rule Encoding · holobiomicslab

   Use when you have untargeted metabolomics data with unknown metabolite structures and need to generate plausible candidate products by systematically applying known enzymatic or chemical transformation rules.
   0 installs
8. ▌
   Chromatographic Method Transfer · holobiomicslab

   Use when you have retention time predictions from a source chromatographic method and need to predict retention times for a target chromatographic method, but have limited calibration data (10–100 molecules) measured on both methods.
   0 installs
9. ▌
   Classifier Prediction Inference · holobiomicslab

   Use when you have a CSV or Excel file containing chemical structure descriptors for one or more molecules, and you want to obtain binary bitter/not-bitter predictions for each molecule using the BitterPredict classifier.
   0 installs
10. ▌
    Confidence Score Interpretation · holobiomicslab

    Use when after executing forward inference on preprocessed mass spectrometry spectra with a deep learning model (e.g., PS²MS), when you have per-spectrum predictions with associated confidence scores or per-class probabilities.
    2 installs
11. ▌
    Cross Language Interface Design · holobiomicslab

    Use when when you have domain-specific functionality (e.g., spectral similarity scoring, peak detection algorithms) implemented in one language (Python) but need to make it callable and composable within an R-based analytical pipeline (Spectra objects);
    0 installs
12. ▌
    Directive Engine Implementation · holobiomicslab

    Use when when you have intermediate JSON data that must be selectively transformed or enriched according to declarative conversion rules—for example, when extracting experimental metadata from tabular spreadsheets, you need to map certain fields to computed or filtered values, apply conditional.
    1 install
13. ▌
    Distribution Channel Validation · holobiomicslab

    Use when when preparing a software release, testing contribution workflows, or auditing package availability: verify that matchms can be installed and imported successfully from all advertised distribution channels (PyPI and Bioconda) to confirm the package metadata, dependencies, and entry points.
    0 installs
14. ▌
    Fdr Correction Multiple Testing · holobiomicslab

    Use when you have computed empirical p-values from randomized sampling (e.
    2 installs
15. ▌
    Functional Group Classification · holobiomicslab

    Use when you have a set of query chemicals (chemical names or structures) and need to match them against a reference chemical library organized by type or category, with the goal of identifying structural similarity, functional group membership, or categorical assignment.
    0 installs
16. ▌
    Gradient Based Saliency Mapping · holobiomicslab

    Use when you have a trained graph neural network model for CCS prediction and need to identify which molecular structural features drive individual predictions or systematic biases.
    0 installs
17. ▌
    Igzip Header Structure Encoding · holobiomicslab

    Use when when implementing an igzip parser, decoder, or validator that must interpret the custom header format; when debugging igzip file corruption or encoding errors; or when extending pymzML's igzip support to handle new index schemes.
    0 installs
18. ▌
    Ion Mobility Reference Matching · holobiomicslab

    Use when you have raw arrival-time data from TWIM-MS and need to convert it to collision cross section (CCS) values for multi-omic analysis.
    1 install
19. ▌
    JSON Schema Output Verification · holobiomicslab

    Use when after extracting tabular data into intermediate JSON form or after applying matrix conversion directives (e.
    0 installs
20. ▌
    Lipid Class Coverage Assessment · holobiomicslab

    Use when when you have acquired a CCS reference library (such as DTCCSN2 for U13C labeled lipids) and need to verify that it contains the expected lipid classes, CCS values are physically plausible for ion mobility data, and coverage matches the library's advertised documentation before using it.
    0 installs
21. ▌
    Lipid Class Stratified Analysis · holobiomicslab

    Use when you have IM-MS lipidomics data with measured CCS values, samples spiked with U13C-labeled lipid internal standards (e.
    0 installs
22. ▌
    Lipid Type Category Enumeration · holobiomicslab

    Use when when you have downloaded or cloned a lipidomics library repository (such as LipidMatch) and need to audit the breadth of lipid-type coverage to ensure the library meets minimum requirements for your analysis scope (e.g., ≥60 distinct lipid categories).
    0 installs
23. ▌
    Mass2motif Network Construction · holobiomicslab

    Use when after MS2LDA has inferred a motifset and you need to visualize and export the relationships between discovered Mass2Motifs for post-processing exploration, comparative annotation, or integration with external tools. Use this skill when you have motifset.json or motifset_optimized.
    0 installs
24. ▌
    Molecular Structure Attribution · holobiomicslab

    Use when you have a trained GNN model predicting CCS values from molecular graphs and need to understand which structural features (node and edge attributes) are most influential for specific predictions or across a test set.
    0 installs
25. ▌
    Multi Key Sorting And Filtering · holobiomicslab

    Use when when converting tabular data to JSON via the matrix directive, you need to exclude records that fail domain-specific validation (e.g., only retain records where a 'test' condition evaluates to true) and/or reorder the output list by one or more fields in ascending or descending order.
    0 installs
26. ▌
    Package Repository Verification · holobiomicslab

    Use when releasing a new version of a Python package to public repositories, when verifying that distribution pipelines are functioning after code changes, or when troubleshooting installation failures reported by users across different platforms (Linux, macOS) or architectures (x86_64, aarch64).
    2 installs
27. ▌
    Peak Removal Robustness Testing · holobiomicslab

    Use when when validating a metabolomics pathway analysis method (particularly decomposition-based approaches like PLAGE) against data quality degradation, or when comparing robustness across methods (PLAGE vs. ORA vs. GSEA).
    0 installs
28. ▌
    Post Hoc Model Interpretability · holobiomicslab

    Use when after training a GNN model on molecular structures with continuous targets (e.g., CCS values), when you need to understand which node-level (atom) or edge-level (bond) features contribute most to individual or aggregate predictions.
    2 installs
29. ▌
    Ppm Tolerance Window Adjustment · holobiomicslab

    Use when a mass spectrum calibration procedure initialized with a narrow ppm window (e.g., ±1.0 or ±5.0 ppm) finds fewer than 5 reference m/z matches.
    0 installs
30. ▌
    Prediction Sensitivity Analysis · holobiomicslab

    Use when you have a trained predictor (like BitterPredict) that accepts structured descriptors and want to understand feature importance without retraining.
    0 installs
31. ▌
    Python Automated Test Execution · holobiomicslab

    Use when when contributing code changes to a Python project (fork, feature branch, or pull request) that uses a setup.py-based test suite, before pushing changes to the remote repository or merging into the main branch.
    0 installs
32. ▌
    Rank Order Correlation Analysis · holobiomicslab

    Use when when you have run a pathway ranking method (such as PALS/PLAGE) on clean metabolomics data and wish to assess how sensitive the resulting pathway activity rankings are to realistic data quality issues—specifically Gaussian noise and random peak dropout—which are prevalent in untargeted.
    0 installs
33. ▌
    REST API Contract Documentation · holobiomicslab

    Use when a webservice component (like MAGMa's joblauncher) lacks formal API documentation but the source code is accessible, and downstream consumers (web applications, external services) need to understand available HTTP endpoints, parameter schemas, and response formats without manual.
    2 installs
34. ▌
    Service Health Check Definition · holobiomicslab

    Use when when deploying a multi-service microarchitecture (such as MAGMa's four distinct subprojects: magmaweb, joblauncher, job, and pubchem) via Docker Compose and you need to ensure that service startup order respects true readiness rather than container existence—particularly when services have.
    0 installs
35. ▌
    Spectral Data Format Validation · holobiomicslab

    Use when after converting existing mass spectrometry formats (mzML, vendor formats) into mzPeak using command-line tools or when receiving mzPeak files from external sources.
    2 installs
36. ▌
    Spectrum Subsetting And Merging · holobiomicslab

    Use when when you have a large MsBackend object and need to (1) select a contiguous or non-contiguous range of spectra for focused analysis, or (2) combine spectra from multiple independently-loaded backends (e.
    1 install
37. ▌
    Structure Organism Pair Binning · holobiomicslab

    Use when when you have loaded a structure-organism pairs table from a natural products database (e.g., LOTUS) and need to answer questions about the distribution of chemical diversity—specifically, how many unique 2D structures appear in exactly 1 organism versus many organisms.
    0 installs
38. ▌
    Binary Spectral Data Extraction · holobiomicslab

    Use when you have parsed imzML XML metadata and loaded the corresponding .ibd binary intensity file, and need to extract specific ion images at one or more target m/z values.
    2 installs
39. ▌
    Bioinformatic Object Conversion · holobiomicslab

    Use when when you have processed Cardinal MSI data (normalized peak intensities, optional SSC segmentation results) and need to transition to Seurat-based workflows for differential expression, pathway analysis, or integration with spatial transcriptomics data.
    1 install
40. ▌
    Blood Sample Handling Protocols · holobiomicslab

    Use when you are planning a blood sampling campaign and need to verify that lipids or polar metabolites of interest will remain stable through your anticipated sample-processing workflow (specific temperature regimes, delays before/after centrifugation).
    0 installs
41. ▌
    Centrality Metric Normalization · holobiomicslab

    Use when after computing raw betweenness centrality scores for metabolites in a bipartite pathway-metabolite igraph network, when you need to identify metabolites with high topological influence for visualization in ranked plots or when comparing centrality across multiple metabolite subsets or.
    0 installs
42. ▌
    Chromatographic Peak Processing · holobiomicslab

    Use when after peak detection when you have a table of detected peaks with m/z values and retention times from LC/HRMS data, and you observe systematic m/z drift across a batch or population-scale study (n > 500 samples).
    0 installs
43. ▌
    Complementary Score Integration · holobiomicslab

    Use when when you have scored a set of potential gene cluster family (GCF)–molecular feature (MF) links using two or more orthogonal methods (e.
    0 installs
44. ▌
    Compound Identifier Aggregation · holobiomicslab

    Use when you have metabolomics results from multiple studies with compound identifiers in heterogeneous formats (names, InChI strings, SMILES, ChEBI/KEGG/HMDB codes) and need to merge datasets for vote-counting or meta-analysis. Apply this skill before computing consensus measures (e.
    0 installs
45. ▌
    Configuration Schema Validation · holobiomicslab

    Use when when you have generated or edited a LipoCLEAN `options.txt` file using `--print MSD4` or `--print MSD5` and need to verify it is well-formed before running the analysis. Use this skill as a pre-flight check before invoking `--options options.
    0 installs
46. ▌
    Consensus Scoring Meta Analysis · holobiomicslab

    Use when when you have harmonized metabolite data from multiple studies with identifier, fold-change direction, and trend classification columns available, but lack standard deviations or variance estimates needed for quantitative meta-analysis.
    0 installs
47. ▌
    Cytoscape Network Format Export · holobiomicslab

    Use when after constructing or filtering a metabolomic network in MetaMapR (e.g., after applying the unique-edges hierarchy filter to resolve multiple edge types between node pairs), and you need to visualize, share, or further analyze the network using cytoscape.js or compatible tools.
    2 installs
48. ▌
    Data Format Compliance Checking · holobiomicslab

    Use when mSMetaEnhancer fetches metadata from external services (CIR, CTS, PubChem, IDSM, BridgeDb) and must write enriched annotations (SMILES, InChI, CAS numbers, formulas, inchikeys, IUPAC names) into .msp files.
    0 installs
49. ▌
    Differential Expression Ranking · holobiomicslab

    Use when you have completed a two-group or multi-group differential expression analysis with computed logFC values (e.
    0 installs
50. ▌
    Docker Image Layer Optimization · holobiomicslab

    Use when you are building a Docker image for a .NET Framework 4.8 application (like AirdPro) that must run on both Windows native containers and Linux+Wine environments, and you need to reduce build time and image size while maintaining separate targets for GUI, CLI, and development modes.
    0 installs
51. ▌
    Dotnet Assembly Path Resolution · holobiomicslab

    Use when your R package wraps a .NET assembly (e.g., RawFileReader) and you need to (1) report to users or logs which assembly file is actually being used, (2) verify that the assembly exists on disk before attempting to invoke it via system calls, or (3) enable diagnostic output showing the exact.
    0 installs
52. ▌
    Drift Correction Across Batches · holobiomicslab

    Use when your preprocessed metabolomics matrix (log2-scaled, with rows as features and columns as samples) exhibits batch-dependent signal drift or technical variation across multiple analytical runs or instrument sessions.
    2 installs
53. ▌
    Eawag Database Rule Application · holobiomicslab

    Use when when you have small-molecule structures (SMILES or structure format) and need to predict their environmental biotransformation pathways under microbial degradation conditions, particularly when the degradation rules must be drawn from curated, experimentally-validated biodegradation.
    1 install
54. ▌
    Enrichment Score Interpretation · holobiomicslab

    Use when after differential expression analysis has produced gene lists with p-values and log fold-change values, and after pathway enrichment tools (clusterProfiler or biotranslator) have computed enrichment scores and adjusted p-values.
    0 installs
55. ▌
    Feature Table Format Conversion · holobiomicslab

    Use when you have raw feature tables exported from NPP tools (XCMS, MZmine 2, MS-DIAL, OpenMS, etc.) in their native formats and need to compare their peak detection and alignment performance against a mzRAPP benchmark dataset.
    0 installs
56. ▌
    Fold Change And P Value Ranking · holobiomicslab

    Use when after performing differential abundance testing (via limma or edgeR) on batch-corrected lipid abundance data, use this skill to rank and filter lipids when you need to prioritize results by both effect size and statistical confidence, especially in complex experimental designs with.
    0 installs
57. ▌
    Fold Change Log2 Transformation · holobiomicslab

    Use when when preparing fold-change measurements from multiple metabolomics studies for quantitative meta-analysis via weighted averaging.
    0 installs
58. ▌
    Force Field Minimization Mmff94 · holobiomicslab

    Use when after RDKit generates multiple 3D conformers from ionized molecular structures using distance-geometry embedding, before filtering with ASE-ANI or submitting to quantum calculations.
    0 installs
59. ▌
    Functional Orthology Annotation · holobiomicslab

    Use when after assigning hierarchical KEGG identifiers to a metabolomics count data frame (via assign_hierarchy with identifier='KEGG'), use this skill when you need to link metabolites to their functional roles (KO numbers) and associated genes for downstream functional analysis, pathway.
    0 installs
60. ▌
    Galaxy Tool Wrapper Development · holobiomicslab

    Use when you have a working R package that performs established preprocessing, analysis, or statistical workflows on formatted tabular data (e.
    2 installs
61. ▌
    Gam Model Diagnostic Evaluation · holobiomicslab

    Use when after fitting candidate GAM splines with B-spline basis functions across a range of basis dimensions (k values 12–20) to anchor feature pairs (m/z and retention time coordinates).
    0 installs
62. ▌
    Ground Truth Ordinal Validation · holobiomicslab

    Use when after running retention-order prediction on a test or evaluation dataset, when you have both predicted retention orderings (from RankSVM, SVR, or similar ordinal regressors) and experimentally validated ground-truth retention orders from the same chromatographic system(s).
    0 installs
63. ▌
    HTTP File Upload Implementation · holobiomicslab

    Use when you are building the initial data ingestion step of a high-throughput MS platform and need to accept raw MS files from users or instruments via a web interface. Use this skill when you require automated validation of vendor-specific formats (Thermo .
    0 installs
64. ▌
    Imzml Continuous Format Parsing · holobiomicslab

    Use when you have acquired raw mass spectrometry imaging data in imzML continuous format (e.g., from CardinalIO or other MSI instruments) and need to load it into R as a structured MSImagingExperiment object to perform statistical analysis, normalization, or visualization.
    2 installs
65. ▌
    Intensity Normalization Spectra · holobiomicslab

    Use when after noise reduction when working with imported imzML MSI data where pixel-to-pixel or sample-to-sample intensity variations due to instrumental sensitivity or sample loading differences must be corrected before mean intensity calculation, ROI analysis, or metabolite annotation.
    0 installs
66. ▌
    Internal Standard Normalization · holobiomicslab

    Use when your metabolomics dataset includes internal standard metabolites (marked in the metabolitedata IS column), log-transformed featuredata are available, and you need to remove systematic variation attributable to instrument drift, sample matrix effects, or batch differences while preserving.
    2 installs
67. ▌
    JSON Table To Matrix Conversion · holobiomicslab

    Use when you have extracted tabular data (e.g., from experimental spreadsheets) in intermediate JSON form with a single table of records, and you need to produce a list of dictionaries (array of objects) for deposition into a data repository such as the Metabolomics Workbench, or when you need to.
    0 installs
68. ▌
    Kegg Data Retrieval And Parsing · holobiomicslab

    Use when when you have selected one or more organisms to analyze and need to extract their complete metabolic reaction and metabolite data from KEGG in order to build a network representation.
    0 installs
69. ▌
    La Icp Ms Isotope Normalization · holobiomicslab

    Use when you have multi-isotope LA-ICP-MS data (e.
    0 installs
70. ▌
    Lc Hrms 2d Area Standardization · holobiomicslab

    Use when after detecting local-maxima in LC-HRMS profile mode datasets and before training or inference with a CNN model for peak classification.
    0 installs
71. ▌
    Linear Regression Model Fitting · holobiomicslab

    Use when when you have a targeted metabolomics dataset with known concentration values for calibration ('curve') and quality control ('qc') samples, peak area intensities for those samples, and you need to establish and validate a concentration-prediction model before applying it to unknown samples.
    0 installs
72. ▌
    Marr Output Object Manipulation · holobiomicslab

    Use when when you have a Marr() output object containing reproducibility statistics computed across replicate experiments and need to reduce dimensionality by retaining only features or sample pairs that meet reproducibility criteria (percentage of reproducible signals exceeding feature-level.
    0 installs
73. ▌
    Mass Difference Adduct Matching · holobiomicslab

    Use when after correlation-based feature pairing has identified feature groups with matching temporal intensity profiles through direct-injection or plasma ionization mass spectrometry experiments. You have a set of putative feature-pair candidates and need to assign specific chemical identities (e.
    0 installs
74. ▌
    Mass Spectrometry Preprocessing · holobiomicslab

    Use when when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) that must be fed into a CNN model for metabolite annotation via compound fingerprint prediction.
    0 installs
75. ▌
    Mass To Charge Ratio Validation · holobiomicslab

    Use when after loading MS-Dial feature tables (e.g., Urine_RP_NEG_norm.txt or Urine_RP_POS_norm.txt) and before sample-level filtering or imputation, whenever the feature abundance matrix contains m/z values acquired across multiple chromatographic runs or polarities.
    1 install
76. ▌
    Mass Tolerance Window Filtering · holobiomicslab

    Use when after calculating neutral mass from observed m/z and adduct type, and before ranking candidates by chemical plausibility. Use it whenever querying a formula database (KEGG, PubChem, or custom) to retrieve all molecular formulae within a specified mass tolerance window of each neutral mass.
    0 installs
77. ▌
    Matlab Workspace Initialization · holobiomicslab

    Use when when you have mass spectrometry imaging root datasets paired with accompanying .mat workspace files (as in the B73 and Oaxacan Green genotypes from Sama et al.
    0 installs
78. ▌
    Matplotlib Figure Customization · holobiomicslab

    Use when when rendering spectrum data (m/z vs. intensity arrays) from MZA files and need to control visual presentation: applying m/z range windows, setting line colors and labels for legend identification, sizing the figure, or choosing between interactive display versus file export.
    2 installs
79. ▌
    Metabolic Marker Identification · holobiomicslab

    Use when after batch effect removal and sample integration, when you have a normalized feature-by-sample abundance matrix (finalData) with corresponding sample group labels (finalLabel), and need to identify which metabolites discriminate between biological conditions or phenotypes for focused.
    2 installs
80. ▌
    Metabolite Database Integration · holobiomicslab

    Use when you need to construct a reference metabolomics database from scratch or when existing public databases (HMDB, MassBank, METLIN) need to be merged into a single queryable resource for metabolite annotation in untargeted mass spectrometry analysis.
    0 installs
81. ▌
    Metabolite Feature M Z Matching · holobiomicslab

    Use when you have (1) a benchmark dataset of known molecules with accurate m/z values, retention time boundaries, and isotopologue identifiers for all enviPat-predicted adducts;
    0 installs
82. ▌
    Metabolite Feature Organization · holobiomicslab

    Use when you have raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z values are features (columns), spatial spots are observations (rows), and intensities form the feature matrix.
    0 installs
83. ▌
    Metabolite Network Construction · holobiomicslab

    Use when when you have a list of input metabolites (e.g., from differential metabolomics analysis) and need to: (1) contextualize them within known metabolic pathways; (2) assess their structural importance in the pathway network rather than statistical significance alone;
    0 installs
84. ▌
    Tensorflow Model Layer Inspection · holobiomicslab

    Use when after converting or downloading a pre-trained Keras model to HDF5 TensorFlow 2.3.0 format, particularly when integrating the model into a fixed-interface pipeline (e.g., NP Classifier) that expects specific named input/output layers.
    0 installs
85. ▌
    Test Result Parsing And Reporting · holobiomicslab

    Use when when you need to validate that a package's periodic integration test suite (distinct from unit tests) passes as expected, or when you must collect and communicate structured evidence of test outcomes across multiple test cases.
    0 installs
86. ▌
    U13c Labeled Lipid Identification · holobiomicslab

    Use when you have measured CCS values from (LC-)IM-MS samples spiked with U¹³C labeled internal standards (e.
    2 installs
87. ▌
    Unit Testing Conditional Branches · holobiomicslab

    Use when when implementing or refactoring a FileInterface._open method or similar polymorphic dispatcher that conditionally instantiates different handler classes based on file extension (e.g., .gz, .db) or format metadata (e.g., indexed gzip detection).
    0 installs
88. ▌
    Validated Link Ranking Comparison · holobiomicslab

    Use when when you have computed multiple independent scoring functions (e.
    0 installs
89. ▌
    Vectorized Operation Verification · holobiomicslab

    Use when when implementing or auditing S4 replacement methods (e.
    3 installs
90. ▌
    Web Service Deployment Validation · holobiomicslab

    Use when when you need to confirm that a publicly hosted academic web service (such as molDiscovery) is live and responding at a documented endpoint URL, or when troubleshooting access issues reported by end users.
    0 installs
91. ▌
    Abstract Syntax Tree Construction · holobiomicslab

    Use when you have a tokenized sequence of domain-specific language tokens and need to construct a hierarchical, unambiguous representation that can be validated against language design principles (expressiveness, precision, scalability, readability) and passed to downstream execution engines.
    0 installs
92. ▌
    Asynchronous Method Introspection · holobiomicslab

    Use when you have a plugin-based converter architecture (e.g., web services and compute libraries in separate directories) and you need to automatically discover all available (source_attribute, target_attribute, converter_name) conversion triples without hardcoding them.
    0 installs
93. ▌
    Basepeak Intensity Identification · holobiomicslab

    Use when when you have Thermo Fisher Scientific .raw files from an Orbitrap instrument and need to identify the m/z value and corresponding intensity of the most abundant ion in each MS1 scan for quality control, method optimization, or feature extraction in a modular R-based proteomics pipeline.
    0 installs
94. ▌
    Biosynformatic Vector Computation · holobiomicslab

    Use when you have a natural product molecule structure in SMILES, InChI, or SDF format and need to convert it into a fixed-length numerical vector representation (fingerprint) that preserves biosynthetic and chemical information for machine learning, similarity searching, or class prediction tasks.
    0 installs
95. ▌
    Candidate Psm Cardinality Control · holobiomicslab

    Use when when rescoring PSMs from a search engine with MS²Rescore and you need to (1) constrain computational cost by reducing the number of candidates fed to feature generators and rescoring engines, (2) control false discovery rate correctly by removing lower-ranking PSMs before final statistical.
    0 installs
96. ▌
    Comparative Performance Profiling · holobiomicslab

    Use when when you have implemented a new or optimized mass spectrometry data processing library and need to demonstrate its computational advantage over established alternatives (e.g., pymzML, pyOpenMS) on real proteomics data. Trigger on availability of: (1) a common input dataset (e.
    0 installs
97. ▌
    Conda Environment File Generation · holobiomicslab

    Use when when you have identified all software dependencies and their exact pinned versions from project documentation (README, setup files, or supplementary materials) and need to create portable environment specifications for a scientific implementation.
    0 installs
98. ▌
    Conda Environment Reproducibility · holobiomicslab

    Use when you have received a conda/pip requirements file (e.g., jestr_requirements.txt) and need to run code that was trained and tested on a specific GPU setup (e.g., NVIDIA A100 with CUDA 11.8).
    0 installs
99. ▌
    Configuration File Interpretation · holobiomicslab

    Use when when you have PSM files from proteomics search engines (MaxQuant, MSGFPlus, Sage, etc.) that use non-standard modification notation (e.g., 'ox', '+57.02146', or mass-shift labels) and need to resccore peptide identifications with MS²Rescore.
    0 installs
100. ▌
     Conformer Ensemble Energy Ranking · holobiomicslab

     Use when after RDKit has generated a large set of 3D conformers for a molecule in SDF or XYZ format, and before submitting conformers to computationally expensive quantum-chemical methods (e.g., QUICK).
     0 installs