← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 11k skills
• 0 followers
• last month last updated

1. ▌
   Empirical Compound Grouping By Adducts And Isotopes · holobiomicslab

   Use when after feature table normalization and imputation are complete, immediately before MS1 and MS2 annotation.
   0 installs
2. ▌
   Feature Network Construction From Mass Spectrometry · holobiomicslab

   Use when you have a preprocessed feature table (tab-delimited: feature ID, m/z, retention time, intensity columns) from LC-MS data and need to annotate which observed features represent the same underlying compound via isotope or adduct relationships.
   0 installs
3. ▌
   Instrumental Parameter Validation Mass Spectrometry · holobiomicslab

   Use when when you have obtained a raw Orbitrap mass spectrometry file and need to verify that the instrument was configured as claimed in the methods section or dataset documentation—especially before investing in peptide fragmentation analysis, spectrum library matching, or quantitative proteomics.
   0 installs
4. ▌
   Interquartile Range Filtering For Outlier Rejection · holobiomicslab

   Use when when you have ensemble predictions (e.g., from Monte-Carlo Dropout inference with N ≥ 10 forward passes per input) and need to distinguish high-confidence from uncertain predictions before downstream analysis.
   0 installs
5. ▌
   Ionization Mode Inference From Acquisition Metadata · holobiomicslab

   Use when when beginning preprocessing of a new LC-MS dataset with mzML files or raw acquisitions and you need to determine which ionization mode was used before running feature detection (Asari) or empirical compound grouping (khipu).
   0 installs
6. ▌
   Mass Spectral Similarity Binning And Stratification · holobiomicslab

   Use when you have predicted structural similarity scores (e.g., Tanimoto or Dice scores) for a large set of spectrum pairs and need to assess prediction accuracy across the full range of possible similarities. Critical when evaluating whether uncertainty filtering (e.
   0 installs
7. ▌
   Naturally Occurring Isotope Contribution Accounting · holobiomicslab

   Use when you have raw fractional abundances of measured isotopologues (FAM) from LC-MS instruments in an isotope labeling experiment and need to correct them to obtain true mass distribution vectors (MDV) reflecting only the contribution from the isotopic tracer.
   3 installs
8. ▌
   Post Translational Modification Pattern Recognition · holobiomicslab

   Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and genomically-predicted precursor peptide sequences, and you need to identify which predicted RiPPs are actually expressed and modified in the sample.
   0 installs
9. ▌
   Precision Recall Curve Generation For Ranking Tasks · holobiomicslab

   Use when when you have computed similarity scores (e.g., MS2DeepScore, Spec2Vec, modified Cosine) between pairs of spectra or compounds and want to compare their ability to retrieve chemically related pairs. Apply this skill if you have ground-truth structural similarity labels (e.
   0 installs
10. ▌
    Probability Threshold Tuning For Chemical Detection · holobiomicslab

    Use when you have a trained NeatMS neural network model (.h5 format) and need to select an operating threshold for peak classification on your LCMS dataset.
    0 installs
11. ▌
    Ranking Metric Computation For Spectral Predictions · holobiomicslab

    Use when after generating ranked predictions of chemical formulas or subformulas for MS/MS spectra (from a neural network model like MIST-CF's formula transformer), compare predicted assignments against ground-truth reference labels to measure ranking quality.
    0 installs
12. ▌
    Smarts Pattern Matching For Chemical Transformation · holobiomicslab

    Use when when you have seed metabolite structures (SMILES or MOL format) from metabolomics data and a curated biotransformation rule database (each rule specifying reactant SMARTS, product SMARTS, and transformation type), and you need to systematically enumerate plausible biotransformation.
    0 installs
13. ▌
    Spectral Annotation Filtering By Similarity Metrics · holobiomicslab

    Use when after running GNPS molecular networking, SIRIUS compound identification, or ISDB in silico annotation on LC-MS/MS data, when you have provisional annotations for features but need to filter them to retain only high-confidence matches before calculating novelty scores, detecting chemical.
    0 installs
14. ▌
    Spectral Annotation Recall Precision Quantification · holobiomicslab

    Use when you have run two or more annotation pipelines on the same MS/MS spectral dataset (e.
    0 installs
15. ▌
    Spectral Peak Retention Signal Noise Discrimination · holobiomicslab

    Use when when you have replicate MS/MS spectra for the same feature (precursor m/z and retention time) and need to distinguish genuine fragment ions from noise.
    0 installs
16. ▌
    Multimodal Spectral Alignment By Molecular Identifier · holobiomicslab

    Use when you have parsed spectral data from four distinct modalities (NMR, HSQC, COSY, IR) stored as separate numpy arrays or DataFrames with normalized chemical shifts and intensity ranges, and you need to create paired multimodal training records where each molecule's spectra across all.
    0 installs
17. ▌
    Tile Matrix Generation Counting Strategy Selection · holobiomicslab

    Use when after importing fragment files into AnnData using pp.import_fragments and before performing spectral embedding (tl.spectral) or other dimension reduction.
    0 installs
18. ▌
    Transcription Factor Cooperative Binding Detection · holobiomicslab

    Use when you have a chromVARDeviations object with precomputed bias-corrected deviations and z-scores for multiple annotation sets (e.
    0 installs
19. ▌
    Variability Score Comparison Across Parameter Sets · holobiomicslab

    Use when when you have computed deviation and variability scores using chromVAR for two or more discrete parameter configurations (e.g., 6-mer vs 7-mer kmers, or different motif databases) and need to determine which parameter set produces stronger or more discriminative variability signals.
    0 installs
20. ▌
    Background Distribution Significance Thresholding · holobiomicslab

    Use when use when the workflow requires background-distribution-significance-thresholding.
    0 installs
21. ▌
    Deep Learning Module Instantiation And Validation · holobiomicslab

    Use when you have cloned or loaded a deep-learning architecture extension (e.g., chemprop-IR) and need to verify that its feature extraction component can be instantiated and produces correctly shaped feature tensors before integrating it into a larger pipeline or training loop.
    0 installs
22. ▌
    Docker Container Runtime Execution And Monitoring · holobiomicslab

    Use when you have a vendor mass spectrometry raw file (e.g., .raw format) that requires conversion to Aird format using AirdPro CLI, and you are running on macOS or Linux.
    0 installs
23. ▌
    Mass Spectrum Noise Threshold Parameter Selection · holobiomicslab

    Use when when processing raw or centroid mass spectra (e.g., ESI-MS or FT-ICR data from Bruker .d or Thermo .raw formats) and you need to remove instrument noise and low-abundance peaks before peak picking or molecular formula assignment.
    0 installs
24. ▌
    Permanova Statistical Testing Multivariate Groups · holobiomicslab

    Use when you have normalized peak intensities or abundance matrices from mass spectrometry (e.
    0 installs
25. ▌
    Shell Environment Setup And Dependency Management · holobiomicslab

    Use when when you need to verify that a GitHub Actions workflow (e.g., main.yml) executes successfully on your local machine, reproduce a reported passing or failing CI build status, or debug why a workflow badge reports success/failure.
    0 installs
26. ▌
    Approximate Nearest Neighbor Indexing For Spectra · holobiomicslab

    Use when when you have a large spectral library (hundreds of thousands or millions of spectra) and need to search unknown query spectra against it for both unmodified and post-translationally modified peptides.
    0 installs
27. ▌
    Background Distribution Generation Shuffled Omics · holobiomicslab

    Use when when training a regression or neural-network model on paired microbiome and metabolome data, and you need to establish a statistically principled cutoff for identifying metabolites (or other features) whose prediction correlations are significantly better than random chance.
    0 installs
28. ▌
    Compound Structure Enumeration Across Generations · holobiomicslab

    Use when you have a set of seed compounds (as SMILES strings) and want to predict downstream products by systematically applying generalized reaction rules (e.g., from MetaCyc) across multiple reaction generations.
    0 installs
29. ▌
    Diffusion Score Normalization With Graph Topology · holobiomicslab

    Use when after propagating diffusion scores through the FELLA metabolite network using set.diffusion, when raw diffusion scores would otherwise favor candidates in high-degree regions or penalize those in sparse regions. Use this normalization when building the final ranked annotation table (Ranked.
    0 installs
30. ▌
    False Discovery Rate Control In Spectral Matching · holobiomicslab

    Use when after performing spectral library matching (whether unmodified or open modification search) and ranking candidate matches by similarity score, apply FDR control when you need to report a curated set of identifications with quantified confidence.
    0 installs
31. ▌
    High Resolution Mass Spectrometry Data Processing · holobiomicslab

    Use when you have uploaded a delimited data file (CSV, TSV, or semicolon-separated) containing at least m/z values and intensity columns from HRMS analysis of a complex sample, and you need to (1) verify that column keywords are correctly recognized, (2) compute derived metrics such as Normalized.
    0 installs
32. ▌
    Mass Spectrometry Feature Intensity Normalization · holobiomicslab

    Use when after aligning raw mass spectra into a 2D feature intensity matrix (features × time points) but before computing pointwise correlation to identify feature pairs with matching temporal profiles.
    0 installs
33. ▌
    Mass Spectrometry Imaging Line Scan Data Handling · holobiomicslab

    Use when you have raw line-scan MSI data from a vendor instrument (Agilent, Bruker, Thermo, or open-source .mzML format) and need to extract ion images for specified m/z targets with spatial binning and tolerance-based filtering.
    0 installs
34. ▌
    Mass Spectrometry Instrument Format Compatibility · holobiomicslab

    Use when you have raw mass spectrometry data from an instrument not yet validated in your pipeline (e.
    1 install
35. ▌
    Meta Analysis Result Visualization Interpretation · holobiomicslab

    Use when after computing a weighted meta-analysis combining p-values, fold-changes, and study sizes across multiple metabolomics studies, you need to identify which metabolites show both statistical significance (p ≤ 0.05) and biological meaningfulness (fold-change ≥ 3.
    0 installs
36. ▌
    Metabolite Count Normalization And Transformation · holobiomicslab

    Use when you have a raw metabolite count data frame (e.g., c57_nos2KO_mouse_countDF) and need to prepare it for univariate statistical testing (e.g., omu_summary with log_transform=TRUE), multivariate analysis (e.g., PCA), or visualization.
    3 installs
37. ▌
    Missing Value Imputation With K Nearest Neighbour · holobiomicslab

    Use when you have log-transformed metabolomics data in SummarizedExperiment format organized as multiple batches, have already filtered metabolites with >50% missing values per batch and retained only those quantified across all batches via intersect method, and now need to impute remaining missing.
    0 installs
38. ▌
    Molecular Formula Representation And Manipulation · holobiomicslab

    Use when you need to represent, validate, and manipulate molecular compositions in MS analysis—specifically when annotating precursor or product ions with elemental formulas, computing monoisotopic masses for formula-to-charge assignments, predicting isotope patterns ([M]+, [M+H]+, [M+Na]+, etc.).
    0 installs
39. ▌
    Multivariate Metabolomic Dimensionality Reduction · holobiomicslab

    Use when when you have a metabolite-pathway association table and per-sample metabolite abundance data (e.
    0 installs
40. ▌
    Probabilistic Classification Network Construction · holobiomicslab

    Use when when you have raw mass spectrometry imaging data tensors and need to build a trainable deep-learning classifier that outputs class probabilities (tumor vs. non-tumor) without preprocessing or manual peak detection.
    0 installs
41. ▌
    Sequencing Adapter Trimming And Quality Filtering · holobiomicslab

    Use when after receiving raw FASTQ files from SRA or local sequencing input, and after FastQC has identified adapter content and quality issues.
    0 installs
42. ▌
    Spatial Coordinate Registration Across Modalities · holobiomicslab

    Use when when you have preprocessed spatial transcriptomics (ST) and spatial metabolomics (SM) datasets in AnnData format with spatial coordinates, and need to align them to a common resolution before joint downstream analysis.
    0 installs
43. ▌
    Species Candidate Ranking From Spectral Alignment · holobiomicslab

    Use when you have an unknown sample spectrum (m/z peaks and intensities from DI-MS, ASAP-MS, or other high-throughput mass spectrometry modalities) and a reference species database of known spectra, and you need to identify the most likely species or authenticate the sample by ranking how well each.
    0 installs
44. ▌
    Statistical Hypothesis Testing Pvalue Computation · holobiomicslab

    Use when after log-transformation and missing-value imputation of a metabolomics featuredata matrix, when you have a design matrix encoding one or more factors of interest and need to test the statistical significance of each metabolite's association with those factors.
    0 installs
45. ▌
    Unified API Design For Heterogeneous Data Sources · holobiomicslab

    Use when your analysis pipeline must ingest mass-spectrometry data from mixed vendor sources (e.g., Thermo RAW, Agilent .d, Waters .raw, and open mzML) without writing separate parser logic for each format.
    0 installs
46. ▌
    Unsupervised Clustering In High Dimensional Space · holobiomicslab

    Use when you have a preprocessed feature matrix from metabolomics data and suspect unknown batch effects, hidden sample substructures, or latent groups not captured by experimental metadata.
    2 installs
47. ▌
    XML Schema Configuration For Bioinformatics Tools · holobiomicslab

    Use when you have a working R package or bioinformatics pipeline (e.g., IonFlow for ionomics analysis) and need to wrap it as a Galaxy tool so that users can invoke it through Galaxy's web interface without direct command-line access. The inputs are tabular datasets (e.
    0 installs
48. ▌
    Hatch Environment Configuration And Activation · holobiomicslab

    Use when you have cloned a Python project (e.g., scverse/scanpy) that includes a hatch.toml configuration file and need to set up a consistent development or testing environment.
    0 installs
49. ▌
    Transcript Quantification Benchmark Comparison · holobiomicslab

    Use when you have two implementations of the same quantification method (or major versions) and observe a persistent disagreement in mapped-read counts, per-read alignment agreement, or abundance correlations on the same reference index and read set.
    0 installs
50. ▌
    Feature Intensity Normalization And Batch Correction · holobiomicslab

    Use when after blank masking and sample dropping, when you have a feature table with intensity values that exhibit systematic variation across sample collection batches or instrument runs.
    0 installs
51. ▌
    Molecular Fingerprint Structural Similarity Tanimoto · holobiomicslab

    Use when when evaluating how well mass spectral similarity scores correlate with actual chemical structure for annotated spectral pairs (e.g., spectra with InChIKey metadata).
    0 installs
52. ▌
    Bayesian Optimization Acquisition Function Selection · holobiomicslab

    Use when after fitting a Gaussian Process regression model to prior LC-MS gradient evaluations (where gradients are encoded as input and separation efficiency is output), use this skill to decide which candidate gradient to test next.
    0 installs
53. ▌
    Correlation Coefficient Computation For Metabolomics · holobiomicslab

    Use when you have an aligned LCMS feature table (output from Eclipse or equivalent alignment tool) and need to identify candidate redundant features for clustering. It is most useful when features are suspected to originate from the same metabolite (e.
    0 installs
54. ▌
    Data Dependent Acquisition Controller Implementation · holobiomicslab

    Use when you have a conceptual MS/MS fragmentation strategy (e.
    0 installs
55. ▌
    Evaluation Data Collection For Simulation Assessment · holobiomicslab

    Use when you are developing or comparing new data-dependent acquisition (DDA) strategies in ViMMS and need to evaluate how well each strategy fragments sampled compounds from the HMDB database.
    0 installs
56. ▌
    High Resolution Mass Spectrometry Data Preprocessing · holobiomicslab

    Use when you have acquired high-resolution MS/MS spectra in mzML, mzXML, or MGF format and need to prepare them for large-scale clustering or similarity searching.
    0 installs
57. ▌
    Mass Spectrometry Peak Filtering And Noise Reduction · holobiomicslab

    Use when you have raw MS/MS spectra in MGF, mzML, or msp format and need to prepare them for mass2motif discovery or topic modeling.
    0 installs
58. ▌
    Metabolic Feature Identification From Tandem Spectra · holobiomicslab

    Use when when processing data with available MS2 spectra (DDA acquisition) after MS1 peak picking has been completed, and you seek to identify additional metabolic features or validate existing peak picking results through MS2 recognition.
    0 installs
59. ▌
    Metabolite Abundance Normalization Across Conditions · holobiomicslab

    Use when you have intracellular metabolomics abundance data (measured metabolite concentrations) from multiple biological replicates collected from two or more cell lines or conditions, and you need to create a normalized, cell-line-level metabolite dataset before computing Reaction Propensity.
    0 installs
60. ▌
    Neural Network Transfer Learning For Spectral Models · holobiomicslab

    Use when your input is a corpus of MS/MS spectra with annotated molecular formulas and adduct types that represent a new ionisation mode, instrument type, or adduct chemistry not well-represented in the pre-trained model's training data. You have access to a trained formula transformer (e.
    1 install
61. ▌
    One Hot Encoding Categorical Chromatography Features · holobiomicslab

    Use when you have raw HPLC column metadata containing categorical fields (e.g., column manufacturer 'Waters', USP type 'L1', solvent identities 'H2O'/'MeOH'/'ACN') that must be converted into numerical representations before featurization for a machine learning pipeline.
    2 installs
62. ▌
    Precision Recall Curve Generation And Interpretation · holobiomicslab

    Use when you have computed spectral similarity scores from multiple methods (e.g., MS2DeepScore, Spec2Vec, modified cosine) on the same set of spectrum pairs, have assigned ground-truth structural similarity labels (e.
    0 installs
63. ▌
    Precision Recall Optimization In Spectral Annotation · holobiomicslab

    Use when you have extracted fragmentation patterns from a collection of MS/MS spectra (using mineMS2) and have partitioned spectra into components via GNPS molecular networking (e.g., connected components, cliques, or high-similarity pairs with cosine > threshold).
    0 installs
64. ▌
    Spectral Feature Clustering By Intensity Correlation · holobiomicslab

    Use when you have an annotated LC-MS feature table with KEGG candidate matches and adduct assignments (output from the matching stage), and you need to disambiguate which features co-elute and correlate in intensity, signaling a common metabolite origin before applying adduct-based filtering.
    0 installs
65. ▌
    Statistical Significance Testing P Value Calculation · holobiomicslab

    Use when after standardizing link scores (strain correlation and IOKR) across all potential GCF-MF pairs in a metabologenomics dataset, perform significance testing to determine whether validated links show statistically distinguishable score distributions from the background.
    0 installs
66. ▌
    Tandem Mass Spectra Structural Similarity Assessment · holobiomicslab

    Use when you have pairs of cleaned tandem mass spectra with known chemical structure annotations (InChIKey, SMILES, or InChI), and you need to predict Tanimoto structural similarity scores directly from spectral data without pre-computing molecular fingerprints.
    0 installs
67. ▌
    Tandem Mass Spectrum Preprocessing And Normalization · holobiomicslab

    Use when you have acquired raw MS/MS spectra (in MGF or mzML format) from a mass spectrometry instrument or public repository (e.g., MassIVE, MetaboLights, GNPS) that will be used for de novo chemical formula ranking or adduct assignment.
    0 installs
68. ▌
    Targeted Metabolite Detection Parameter Optimization · holobiomicslab

    Use when when you have centroided .mzML LC–MS runs and a target list (compound ID, theoretical m/z, expected RT, polarity) but are uncertain whether your m/z and RT windows are wide enough to capture all targets without false positives.
    0 installs
69. ▌
    Molecular Geometry Neural Network Potential Evaluation · holobiomicslab

    Use when after RDKit has generated multiple conformations for a molecule in an SDF or XYZ format, and you need to reduce the conformational ensemble to a tractable size (by energy-based ranking) before submitting to expensive quantum-chemical calculations (e.g., QUICK).
    0 installs
70. ▌
    Biosynthetic Gene Cluster Detection And Annotation · holobiomicslab

    Use when you have assembled microbial genomes (nucleotide FASTA files) and want to identify biosynthetic potential and group related BGCs for downstream linking with metabolomic data;
    0 installs
71. ▌
    CLI Application Invocation With File Io Management · holobiomicslab

    Use when when you have vendor mass spectrometry raw files (e.g., .raw format) that must be converted to an open format (Aird) using a Windows .
    2 installs
72. ▌
    Mass Spectrometry Visualization Backend Comparison · holobiomicslab

    Use when you have a mass spectrometry visualization library that claims to support multiple plotting backends and need to verify that: (1) all backends produce functionally equivalent outputs, (2) execution times are consistent with reported benchmarks, and (3) the library scales appropriately.
    0 installs
73. ▌
    Molecular Property Prediction Feature Construction · holobiomicslab

    Use when when you have molecular structures (SMILES or graph formats) and need to predict a physicochemical or spectral property (e.g., infrared spectra) using a graph neural network architecture. Use this skill when the base model architecture (e.
    2 installs
74. ▌
    Over Representation Analysis Pvalue Interpretation · holobiomicslab

    Use when when you have run ORA on a metabolomics dataset and obtained p-values for pathway enrichment, but you need to assess whether observed significance is genuine or an artifact of incomplete metabolite coverage.
    0 installs
75. ▌
    Retention Time Abundance Correlation Visualization · holobiomicslab

    Use when after applying AbundanceSimilarityParam (with threshold ≥0.7 and log2 transform) to retention-time-based feature groups from SimilarRtimeParam, when you need to examine the internal correlation structure of specific feature sub-groups (e.g., FG.
    0 installs
76. ▌
    Structure Organism Pair Counting And Deduplication · holobiomicslab

    Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) in TSV or CSV format with separate 2D and 3D structure-organism pair tables, and need to produce authoritative headline counts of unique referenced pairs, unique curated structures, unique organisms, and source.
    0 installs
77. ▌
    Approximate Nearest Neighbor Indexing Construction · holobiomicslab

    Use when when you have a large spectral library (hundreds of thousands to millions of spectra) and need to perform open modification searching on query spectra where exhaustive comparison against all library entries is computationally prohibitive.
    0 installs
78. ▌
    Coefficient Of Variation Calculation And Filtering · holobiomicslab

    Use when after loading and applying minimum non-missing-value thresholds to an omics expression dataset (proteomics, metabolomics, or other panomics data).
    2 installs
79. ▌
    Correlation Coefficient Computation Across Samples · holobiomicslab

    Use when after XCMS feature detection and retention time correction, when you need to group features derived from the same compound. Features from the same compound show correlated quantitative trends across samples;
    1 install
80. ▌
    Data Quality Assessment From Molecular Descriptors · holobiomicslab

    Use when processing spectral datasets from open mass spectra libraries (OMSLs) where structural identifiers and ionization metadata are incomplete or inconsistent.
    0 installs
81. ▌
    Dimensionality Reduction And Clustering Evaluation · holobiomicslab

    Use when you have high-dimensional feasible flux distributions sampled from constraint-based metabolic models for multiple biological samples (e.
    0 installs
82. ▌
    Flux Distribution Interpretation Across Cell Lines · holobiomicslab

    Use when you have sampled 10,000+ steady-state flux solutions for each of multiple cell lines from a constraint-based model; computed Reaction Propensity Scores (RPS) from substrate abundance (metabolomics) and Reaction Activity Scores (RAS) from gene expression (transcriptomics);
    0 installs
83. ▌
    Gzip Compression With Random Access Implementation · holobiomicslab

    Use when you have a large text or structured file (mzML, XML, plain text) that you want to compress while retaining the ability to retrieve specific logical blocks (chapters, spectra, records) by identifier without decompressing the entire file.
    0 installs
84. ▌
    Hierarchical Clustering Euclidean Complete Linkage · holobiomicslab

    Use when you have a normalized microbe-metabolite feature attribution score matrix (rows = microbes, columns = metabolites) and need to explore hierarchical structure and visually assess similarity patterns before determining the optimal number of clusters via consensus clustering.
    0 installs
85. ▌
    Hypergeometric Distribution Null Model Application · holobiomicslab

    Use when when you have raw strain correlation scores computed across multiple GCF–MF link pairs from a metabologenomics dataset and need to compare score magnitudes across different links.
    0 installs
86. ▌
    Message Passing Neural Network Architecture Design · holobiomicslab

    Use when when you have a working base MPNN implementation (e.g., chemprop) and need to adapt it for a new molecular property target (e.g., spectral data) that requires custom input processing, intermediate feature representations, or output layer modifications beyond the original model's scope.
    0 installs
87. ▌
    Multi Modal Spot Validation And Quality Assessment · holobiomicslab

    Use when after performing spot_align_byknn to map SM spots to ST spots, validate that all SM spots have been successfully assigned and that the Euclidean distance distributions between SM spots and their assigned nearest ST neighbors are reasonable (no outliers or failed assignments that would.
    0 installs
88. ▌
    Multiple Testing Correction And P Value Adjustment · holobiomicslab

    Use when when you have generated raw p-values from differential expression analysis on preprocessed count matrices (mRNA, miRNA, isoforms, lipids, or proteins) using edgeR, DESeq2, or RankProduct and need to identify statistically significant features while controlling familywise error rate or.
    2 installs
89. ▌
    Organism Context Metabolic Plausibility Assessment · holobiomicslab

    Use when when BioTransformer or another metabolism predictor has generated a list of candidate metabolite structures (in SMILES or InChI format) for a query compound, and you need to identify which candidates are most likely to occur in a specific organism or environment (e.
    0 installs
90. ▌
    Peak Parameter Optimization For Targeted Compounds · holobiomicslab

    Use when you have centroided high-resolution Orbitrap or GC-CI-MS mzML files and a formulaTable of target compounds with known m/z, retention time, and molecular formula, and you need to extract isotopologue abundances and quantification metrics (area, maxo intensity, ppm error) for each labeled.
    2 installs
91. ▌
    Plant Species Authentication Via Mass Spectrometry · holobiomicslab

    Use when when you have mass spectrometry raw data (DI-MS or ASAP-MS format) from plant samples that are easily confused due to morphological similarity, or when you need to verify or authenticate the species identity of a plant material against a reference database.
    0 installs
92. ▌
    Redundancy Filtering In Biosynthetic Gene Clusters · holobiomicslab

    Use when when you have a collection of tokenised BGCs (represented as combinations of Pfam domains and subPfams) that may contain redundant or near-identical sequences, and you need to reduce computational burden and avoid biased sub-cluster detection caused by over-representation of similar BGCs.
    0 installs
93. ▌
    Singularity Container Image Building And Execution · holobiomicslab

    Use when you have a Docker image published to a registry (e.g., docker://stravsm/msnovelist6), need to run it on an HPC cluster with SLURM scheduling, and must allocate specific hardware resources (GPUs, RAM) per job.
    0 installs
94. ▌
    Sphinx Gallery Execution And Performance Profiling · holobiomicslab

    Use when you have a Sphinx-based documentation project with multiple gallery scripts (e.
    0 installs
95. ▌
    Validation Test Design For Biochemical Identifiers · holobiomicslab

    Use when you have implemented or integrated a biochemical identifier converter (e.
    0 installs
96. ▌
    Weighted Correlation Network Module Interpretation · holobiomicslab

    Use when after WGCNA has identified and named metabolic correlation modules from preprocessed, normalized, and imputed metabolomic data, and you need to test whether specific modules show statistically significant association with a known sample grouping (e.
    0 installs
97. ▌
    Z Score Normalization For Cross Dataset Comparison · holobiomicslab

    Use when you have multiple scoring functions (e.g., strain correlation or spectral similarity scores) computed over heterogeneous GCF-MF or BGC-spectrum link sets where raw scores cannot be directly compared due to differences in set sizes (GCF size g, MF size m, overlap o) or null-model.
    0 installs
98. ▌
    Nearest Neighbor Graph Construction Pynndescent · holobiomicslab

    Use when when analyzing spatial molecular data (e.g., from tissue sections or microscopy) where you need to build k-nearest neighbor graphs on high-dimensional coordinate arrays (n_obs × n_dims) and exact nearest neighbor computation is too slow or memory-intensive;
    2 installs
99. ▌
    Reduction Plot Interpretation And Visualization · holobiomicslab

    Use when after computing gene set enrichment scores (e.g., via GESECA on reverse PCA feature loadings) on a single-cell or bulk dataset with an existing dimensionality reduction (tSNE, UMAP, PCA).
    0 installs
100. ▌
     Statistical Precision Comparison Ranked Outputs · holobiomicslab

     Use when when a statistical method offers a parameter to trade computational cost for precision (e.
     0 installs