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HolobiomicsLab

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1. ▌
   Spectral Peak Binning Preprocessing · holobiomicslab

   Use when when you have raw high-resolution tandem mass spectra (mzML, mzXML, or MGF format) that you intend to cluster or compare at scale, and you need to convert continuous m/z and intensity measurements into discrete bins suitable for feature hashing or similarity searching.
   2 installs
2. ▌
   Spectral Peak Intensity Aggregation · holobiomicslab

   Use when you have multiple replicate MS/MS spectra for the same metabolic feature (e.g., 66 top-TIC spectra for feature 1982) and need to identify robust peaks by merging nearby m/z values and pooling their signal strength.
   0 installs
3. ▌
   Spectral Quality Control Assessment · holobiomicslab

   Use when after MS1 extraction (coarse/fine error correction, EIC window extraction) and retention time windowing on a set of mzML files tagged with ionization mode and compound adducts.
   2 installs
4. ▌
   Spectral Scan Generation And Export · holobiomicslab

   Use when you have real LC-MS/MS data (mzML) from a complex sample (e.g., beer, metabolomics extract) and need to prototype or validate a new data-dependent acquisition (DDA) strategy—such as Top-N fragmentation—before deploying it on physical instrumentation.
   0 installs
5. ▌
   Spectral Vectorization For Indexing · holobiomicslab

   Use when when you have a collection of MS/MS reference spectra and unknown query spectra that must be rapidly matched against a large spectral library, and you need to enable approximate nearest neighbor indexing to reduce computational cost from exhaustive pairwise comparison to K-nearest neighbor.
   0 installs
6. ▌
   Spectrum Pair Retrieval And Ranking · holobiomicslab

   Use when you have a test set of annotated MS/MS spectra with known structural similarity (via molecular fingerprints or InChIKey), and you want to assess how well a spectral similarity measure (learned or classical) retrieves structurally related compound pairs across a full range of thresholds.
   0 installs
7. ▌
   Substructure Annotation Integration · holobiomicslab

   Use when you have (1) a GNPS molecular network (classical or feature-based) with cluster/feature identifiers, (2) MS2LDA output containing Mass2Motif assignments with probability and overlap scores for those same clusters/features, and (3) a goal to annotate network nodes with substructural and.
   0 installs
8. ▌
   Table Join Alignment On Identifiers · holobiomicslab

   Use when you have a feature quantification table output from MZmine3 feature detection (rows = features, columns = sample abundance values) and a separate sample metadata file (rows = samples, columns = sample attributes) that need to be unified before downstream statistical analysis, data cleanup.
   1 install
9. ▌
   Tandem Mass Spectra Standardization · holobiomicslab

   Use when you have acquired raw tandem MS data from ProteomeXchange or vendor instruments in proprietary formats (e.g., Thermo .raw files) and need to perform comparative clustering benchmarks or quality assessments across multiple clustering tools.
   0 installs
10. ▌
    Targeted Transition List Generation · holobiomicslab

    Use when you have a set of lipid targets defined by species name, acyl chain composition, and expected adducts, and you need to configure a targeted mass spectrometry workflow (PRM or MRM) in Skyline.
    2 installs
11. ▌
    Technical Replicate Signal Modeling · holobiomicslab

    Use when your LCMS metabolomics dataset exhibits run-order-dependent intensity drift (signal decay or gain over the course of a sample batch), you have pooled technical replicates (identical biospecimen injected multiple times across the run sequence) and/or known internal standard compounds, and.
    0 installs
12. ▌
    Theoretical Fragment Ion Generation · holobiomicslab

    Use when when you have a peptide sequence and need to predict its fragment ion spectrum for stable isotope labeling validation, particularly when comparing against observed mass spectrometry data with natural or enriched isotopic abundance (e.g., 1% or 50% 13C incorporation).
    0 installs
13. ▌
    Throughput Optimization Ms Querying · holobiomicslab

    Use when you have experimental MS/MS spectra that must be matched against a large hierarchical fragmentation library (e.g., 168.
    0 installs
14. ▌
    Time Series Intensity Normalization · holobiomicslab

    Use when when LCMS metabolomics abundance tables show systematic intensity drift across the injection sequence (e.g., instrument signal decay or gain over hours), and you have pooled technical replicate injections and/or internal standard compounds distributed throughout the run.
    0 installs
15. ▌
    Tracer Impurity Correction Modeling · holobiomicslab

    Use when when processing LC-MS data from isotope labeling experiments where the tracer (13C, 2H, 15N, 18O, or 34S) has known isotopic impurity and you observe discrepancies between measured isotopologue abundances (FAM) and expected labeling patterns.
    1 install
16. ▌
    Transition Group Feature Extraction · holobiomicslab

    Use when when you have loaded a TransitionGroup (extracted ion chromatogram or mobilogram from DIA mass spectrometry data) and need to identify precise peak boundaries, apex retention/drift time, and intensity values for quantitative feature detection.
    0 installs
17. ▌
    Untargeted Lc Ms Data Preprocessing · holobiomicslab

    Use when when you have raw untargeted LC-MS metabolomics data and need to detect low-quality or mis-integrated peaks in an XCMS-processed xcmsSet object before performing metabolite annotation, statistical analysis, or biomarker discovery.
    0 installs
18. ▌
    Virtual Chemical Mixture Generation · holobiomicslab

    Use when you need to create a synthetic chemical population for testing data-dependent acquisition (DDA) strategies in a simulation environment before committing to real mass spectrometry analysis.
    0 installs
19. ▌
    Workflow Architecture Documentation · holobiomicslab

    Use when you need to understand how a complex MS/MS spectral search system routes query spectra through multiple parallel processing pipelines with different objectives (e.g., reliable exact matching vs. fast approximate matching).
    0 installs
20. ▌
    Workflow Reproducibility Validation · holobiomicslab

    Use when after implementing or deploying a containerized Nextflow workflow that processes LC-HRMS metabolomics .
    2 installs
21. ▌
    Xcms Grouping Result Interpretation · holobiomicslab

    Use when xCMS grouping has been performed on LC-MS data from studies with hundreds of samples or data acquisition periods longer than a week, where retention time drift structures are complex and the single-warping-function assumption is likely violated.
    0 installs
22. ▌
    Browser Security Policy Configuration · holobiomicslab

    Use when you need to run a web application locally (by opening index.html directly in the browser) and the application uses WebWorker or WebAssembly modules that fail to load with cross-origin policy or file-access errors.
    2 installs
23. ▌
    Cumulative Distribution Visualization · holobiomicslab

    Use when when you have per-feature quality metrics (such as CV values from NMR or MS reproducibility analysis) and need to: (1) confirm that a specified proportion of features meet regulatory thresholds (e.g., 99% < 0.30, 92% < 0.15 for CV);
    2 installs
24. ▌
    Deep Learning Spectral Language Model · holobiomicslab

    Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format with mandatory PRECURSOR_MZ and IONMODE tags) and need to identify structurally related metabolites from a reference database.
    0 installs
25. ▌
    Memory Mapped File Selection Strategy · holobiomicslab

    Use when initializing a Dataset object in NMRFx and must decide which storage backend to use for in-memory or memory-mapped file access.
    1 install
26. ▌
    Peak Network To Metabolite Assignment · holobiomicslab

    Use when after peak clustering has produced peak network groups (ideally from the same compound) and you need to assign chemical identities.
    0 installs
27. ▌
    Repository Cloning And Initialization · holobiomicslab

    Use when you have a GitHub repository URL, a documented Python version requirement, and a list of pinned package versions, and you need to verify that the application will initialize without import or runtime errors before proceeding to data analysis or method replication.
    2 installs
28. ▌
    Spectral Similarity Scoring Parent Tp · holobiomicslab

    Use when after generating TP candidates (via in-silico prediction or library lookup) and extracting MS/MS peak lists for both parent features and TP feature candidates, use spectral similarity scoring to quantify fragmentation pattern overlap.
    0 installs
29. ▌
    Summarized Experiment Object Handling · holobiomicslab

    Use when you have cross-validated, filtered metabolomic NMR or MS data in a SummarizedExperiment container and need to prepare it for metabolome-wide association studies (MWAS) with epidemiological confounders.
    2 installs
30. ▌
    Top K Accuracy Ranking And Evaluation · holobiomicslab

    Use when a machine learning model produces multiple ranked predictions (each with an associated confidence score) for a single input, and you need to quantify how often the correct answer appears in the top-k predictions.
    0 installs
31. ▌
    Transformer Cnn Hybrid Model Training · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data with compound labels and need to identify multiple compounds in a flavor mixture where both local spectral patterns (handled by CNN) and long-range spectral dependencies (handled by Transformer) are diagnostic.
    0 installs
32. ▌
    Anndata Backed Object Manipulation · holobiomicslab

    Use when when working with large single-cell ATAC-seq or multi-omics datasets where in-memory storage is infeasible (>1M cells), and you need to iteratively add or modify count matrices (tile-based, peak-based, or gene-based) while preserving fragment-level data for reproducibility and re-analysis.
    0 installs
33. ▌
    Differential Tf Occupancy Analysis · holobiomicslab

    Use when you have aligned ATAC-seq BAM files and peak annotations from two or more experimental conditions (e.
    0 installs
34. ▌
    Genomic Feature Annotation Overlap · holobiomicslab

    Use when after you have identified a set of differentially methylated bases or regions (e.
    0 installs
35. ▌
    Hi C Fastq To Contact Map Pipeline · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a sequencing experiment and need to generate kilobase-resolution Hi-C contact maps conforming to ENCODE reference standards.
    0 installs
36. ▌
    Hic Contact Map Feature Annotation · holobiomicslab

    Use when you have completed Hi-C map generation (producing .hic files from aligned reads) and need to detect and annotate topological features such as chromatin loops, topologically associating domains (TADs), or interaction peaks.
    1 install
37. ▌
    Illumina 450k Epic Dataset Loading · holobiomicslab

    Use when you have raw .idat files or a beta-valued matrix from an Illumina HumanMethylation450 or EPIC array experiment and need to import the full probe set into R for downstream quality control, normalization, and differential methylation analysis.
    0 installs
38. ▌
    Methylation Batch Effect Detection · holobiomicslab

    Use when you have loaded a normalized beta-valued methylation matrix (e.
    0 installs
39. ▌
    Methylation Probe Count Validation · holobiomicslab

    Use when immediately after loading raw methylation array data using champ.load() or champ.import() to verify data integrity.
    2 installs
40. ▌
    Module Import And API Verification · holobiomicslab

    Use when before invoking any Python module in a multi-step Hi-C processing pipeline, or when a dependency has been freshly installed or reinstalled.
    0 installs
41. ▌
    Paired Insertion Counting Strategy · holobiomicslab

    Use when you have loaded fragment data from single-cell ATAC-seq experiments into a backed AnnData object (with fragments stored in .obsm['fragment_paired'] or .
    1 install
42. ▌
    Peak Calling Output Interpretation · holobiomicslab

    Use when you have run a peak-calling algorithm on sparse CUT&RUN bedGraph data and received a BED-format output file;
    0 installs
43. ▌
    System Dependency Version Checking · holobiomicslab

    Use when you are preparing to run a complex multi-tool bioinformatics pipeline (such as HiC-Pro) on a new system or cluster, and need to confirm that all required binaries exist in the execution environment and meet minimum version thresholds (e.g., samtools >=1.9, Python >3.
    0 installs
44. ▌
    Assembly Version String Retrieval · holobiomicslab

    Use when when you need to validate that a .NET assembly (such as ThermoFisher.CommonCore.RawFileReader) is correctly installed and accessible before attempting data reading operations.
    0 installs
45. ▌
    Atom Feature Extraction Chemistry · holobiomicslab

    Use when you have canonicalized SMILES strings from a chemical database (e.
    2 installs
46. ▌
    Bayesian Meta Learning Projection · holobiomicslab

    Use when you need to transfer retention time predictions from one chromatographic method to another, but have access to only a small number (≥10) of molecules with known retention times in both methods.
    0 installs
47. ▌
    C Sharp Wrapper Method Validation · holobiomicslab

    Use when when integrating an R package that wraps a compiled .NET assembly (such as rawrr), you need to verify that the internal dispatch mechanism between the R layer and the C# layer is operational before attempting to read actual raw data files.
    0 installs
48. ▌
    Calibration Curve Fitting Ms Data · holobiomicslab

    Use when you have raw mass spectrometry intensity data from targeted analytes and a set of calibration standard measurements with known concentrations.
    2 installs
49. ▌
    Chemodiversity Metric Calculation · holobiomicslab

    Use when when you have sum-normalized peak-abundance matrices from FT-ICR MS data with assigned molecular formulas and need to compare metabolite diversity between treatment groups (e.g., inoculated vs. control samples).
    0 installs
50. ▌
    Conditional Dependency Resolution · holobiomicslab

    Use when a Python library exposes functionality that depends on external packages (like sqlalchemy, pandas, or lxml) that are not required for core operations.
    2 installs
51. ▌
    Container Image Size Verification · holobiomicslab

    Use when after completing a multi-stage Docker build targeting a compiled runtime environment (e.g., airdpro:cli produced from a Wine + .NET Framework 4.8 + Ubuntu 22.
    0 installs
52. ▌
    Count Verification And Validation · holobiomicslab

    Use when you have grouped unique 2D chemical structures by organism prevalence and need to confirm that the counts in each frequency bin (singleton, low-diversity, medium-diversity, high-diversity) match published or curated reference values.
    0 installs
53. ▌
    Cross Domain Masst Output Parsing · holobiomicslab

    Use when you have executed batch searches against one or more domain-specific MASST tools and received multiple output files (_microbe.html, _plant.html, _tissue.html, _microbiome.html, _food.html, _matches.tsv, _library.tsv, _datasets.tsv, _count_*.
    0 installs
54. ▌
    Custom Metabolite Set Integration · holobiomicslab

    Use when you have a user-supplied metabolite set file (CSV or JSON) defining custom groupings of metabolites (e.
    0 installs
55. ▌
    Dataframe Lazy Loading Comparison · holobiomicslab

    Use when when designing or optimizing an MsBackend implementation (or similar columnar data structure) you must decide whether to pre-allocate all known columns in the backing DataFrame at initialization or defer column creation until first access.
    0 installs
56. ▌
    Docker Multistage Build Execution · holobiomicslab

    Use when you need to containerize a C#-based Windows application (like AirdPro CLI) for Linux deployment, require Wine and .NET Framework 4.
    2 installs
57. ▌
    Dotnet Assembly Path Verification · holobiomicslab

    Use when when you have just loaded the rawrr R package and need to confirm that the bundled .NET 8.0 assembly (rawrr.exe) is present and functional before performing any mass spectrometry data extraction operations.
    0 installs
58. ▌
    Environment Variable Provisioning · holobiomicslab

    Use when when extending a multi-service project (like MAGMa with its four subproject components) to container orchestration, and you need to ensure each microservice (magmaweb, joblauncher, job, pubchem) receives the correct configuration—such as port mappings, service URLs, and data paths—without.
    0 installs
59. ▌
    File Format Compliance Validation · holobiomicslab

    Use when you have generated or received mzPeak files from a Rust, Python, R, or other implementation and need to verify they comply with the published HUPO-PSI specification before integration into a production workflow, data repository, or downstream analysis pipeline.
    1 install
60. ▌
    Ftms Mass Spectrum Peak Detection · holobiomicslab

    Use when you have loaded an FT-ICR raw spectrum (e.g., ESI_NEG_SRFA.d in Bruker or ThermoFisher .raw format) and need to identify the m/z positions and intensities of individual mass spectral peaks.
    1 install
61. ▌
    Github Actions Artifact Retrieval · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as a development build release pipeline) has completed successfully, capture its build artifacts (installers, portable binaries, or packages), and document the workflow run metadata.
    0 installs
62. ▌
    Github Actions Workflow Execution · holobiomicslab

    Use when you need to validate that a repository's automated build, test, or publish pipeline is functioning correctly on a target branch (e.g., release branch); when you want to confirm that workflow status badges in documentation accurately reflect current execution state;
    0 installs
63. ▌
    Hex Dump Parsing And Verification · holobiomicslab

    Use when when implementing or reverse-engineering a custom binary file format (e.
    0 installs
64. ▌
    Installation Validation Reporting · holobiomicslab

    Use when when deploying a new Python package in a reproducible analysis environment or continuous integration pipeline, and you need to confirm that all required core modules (e.g., pyteomics.mass, pyteomics.pepxml, pyteomics.mzid, pyteomics.tandem, pyteomics.
    0 installs
65. ▌
    Inter Sample Variance Calculation · holobiomicslab

    Use when after applying batch correction (e.g., via pycombat) to a multi-batch feature table, to validate whether the correction has reduced systematic intensity differences between batches.
    0 installs
66. ▌
    Mass Spectrometry Query Semantics · holobiomicslab

    Use when when you need to enable users to express complex mass spectrometry search patterns (e.
    0 installs
67. ▌
    Memory Profiling And Benchmarking · holobiomicslab

    Use when when designing or optimizing backends that handle large MS datasets (mzML, mzXML, CDF files via MsBackendMzR), to verify that claimed memory advantages of on-disk or chunked approaches actually materialize in practice.
    0 installs
68. ▌
    Metabolite Target List Formatting · holobiomicslab

    Use when you have a raw LC–MS compound metadata file (xlsx or csv) with heterogeneous column names and column order, and you need to prepare it for targeted peak detection in TARDIS.
    2 installs
69. ▌
    Model Generalizability Assessment · holobiomicslab

    Use when you have a pre-trained GNN model for CCS prediction and need to verify that it generalizes to test data that was held out during training. Use it specifically when comparing model performance across different molecular datasets (e.
    0 installs
70. ▌
    Molecular Fingerprint Computation · holobiomicslab

    Use when you have natural product molecules (or compounds from natural product-like databases such as COCONUT or ZINC) in structural format (SMILES, InChI, or SDF file) and need a fingerprint representation optimized for biosynthetic-class prediction, structural clustering, or bioinformatic feature.
    0 installs
71. ▌
    Multi Inheritance Class Hierarchy · holobiomicslab

    Use when when you need to support multiple plotting library backends (static or interactive) for the same data visualization domain (e.
    0 installs
72. ▌
    Multi Service Integration Testing · holobiomicslab

    Use when when building or modifying an asynchronous annotation pipeline that dispatches metadata enrichment requests to multiple heterogeneous web services and must verify that each service's HTTP calls succeed, response parsing is correct, and enriched fields are correctly merged into the output.
    0 installs
73. ▌
    Mzml Data Parsing Pymzml Pyopenms · holobiomicslab

    Use when you have mzML-format mass spectrometry data files and need to load them into memory as structured data (pandas DataFrame) to prepare for visualization with pyOpenMS-Viz or other analysis pipelines.
    1 install
74. ▌
    Numerical Reproducibility Testing · holobiomicslab

    Use when you have instantiated a learned component (embedding layer, encoder, or transformer submodule) from a published codebase and need to verify that its forward pass produces outputs matching the original paper's implementation before integrating it into a downstream analysis pipeline.
    0 installs
75. ▌
    Package Manager Environment Setup · holobiomicslab

    Use when when you need to establish a working installation of a Python package in a fresh or isolated environment, particularly when the package is available through multiple distribution channels (PyPI, Bioconda, AUR) and you want to verify that the installation is complete and functional before.
    1 install
76. ▌
    Pathway Rank Stability Assessment · holobiomicslab

    Use when when you have completed a PALS pathway analysis on a clean metabolomics peak intensity matrix and pathway annotation set, and you need to verify that the ranked pathway discoveries are not artifacts of favorable data quality.
    2 installs
77. ▌
    Python Class Discovery Reflection · holobiomicslab

    Use when when building an extensible converter framework where new converter implementations (e.g., WebConverters or ComputeConverters for external chemical services) should be automatically discovered and registered without modifying a central registry.
    0 installs
78. ▌
    Quality Control Metric Evaluation · holobiomicslab

    Use when you have measured IM-MS lipidomics data spiked with U13C labeled internal standards and need to assess whether CCS bias remains within acceptable limits for each lipid class-adduct combination.
    0 installs
79. ▌
    R Package Loading And Diagnostics · holobiomicslab

    Use when when deploying an R package from a non-CRAN repository (e.g., r-universe, Bioconductor, GitHub), or when verifying that a package build is reproducible and meets CRAN submission standards prior to integration into a larger analysis pipeline.
    0 installs
80. ▌
    Record Identifier Mapping To JSON · holobiomicslab

    Use when when you have a tagged tabular file (Excel or CSV) with columns marked using export tag syntax (e.g., #study.id, #subject.id, #.
    0 installs
81. ▌
    Script Execution Time Measurement · holobiomicslab

    Use when you have a set of gallery or example scripts that must run consistently across multiple backend implementations (e.g., matplotlib, Bokeh, Plotly), and you need to verify that reported execution times are accurate or detect performance changes.
    0 installs
82. ▌
    Software Component Identification · holobiomicslab

    Use when when you need to understand the modular structure of a multi-component research software project—particularly when integrating, documenting, or extending a system whose architecture is not immediately obvious from high-level descriptions.
    0 installs
83. ▌
    System Library Dependency Mapping · holobiomicslab

    Use when a Shiny application or similar cross-platform tool is restricted to a single operating system (e.
    0 installs
84. ▌
    Metabolite Feature Quality Control · holobiomicslab

    Use when you have a metabolomic SummarizedExperiment object with replicate QC (quality control) samples and need to remove non-reproducible metabolic features before phenotype association modeling. Use it specifically when your workflow requires FDA-compliant reproducibility thresholds (CV < 0.
    0 installs
85. ▌
    Model Metadata Schema Verification · holobiomicslab

    Use when before submitting peak data or other inputs to a machine learning classification API for the first time, after a model update, or if you encounter unexpected prediction errors. It is essential when the underlying model's input names or structure may change and require code updates.
    2 installs
86. ▌
    Nmr Spectra Deep Learning Encoding · holobiomicslab

    Use when when you have preprocessed 1H NMR spectral data from flavor mixtures or similar compound identification tasks, and you need to identify which compounds are present.
    0 installs
87. ▌
    Nv Header Structure Interpretation · holobiomicslab

    Use when you have a raw NV file from NMRViewJ or compatible NMR acquisition software and need to extract header metadata before processing spectroscopic data.
    0 installs
88. ▌
    Pathway Ranking And Prioritization · holobiomicslab

    Use when after peak annotation when you have: (1) a peak intensity matrix (rows=peaks with KEGG/ChEBI/UniProt IDs, columns=samples) with group labels; (2) a pathway database (KEGG, Reactome, or user-defined metabolite sets); (3) a comparative experimental design (case vs. control groups).
    2 installs
89. ▌
    Peak Network Clustering Inadequate · holobiomicslab

    Use when you have picked peaks (coordinates and intensities) from INADEQUATE spectra and need to distinguish which peaks likely originate from the same metabolite before matching to a reference database.
    0 installs
90. ▌
    Transformer Architecture Inference · holobiomicslab

    Use when you have acquired or generated multi-modal spectroscopic data (integrated NMR, HSQC, COSY, IR spectra) in the model's expected input format, a pre-trained MultiModalSpectralTransformer checkpoint is available, and you need to predict molecular structures from these spectra without.
    0 installs
91. ▌
    Bam To Fragment File Conversion · holobiomicslab

    Use when when you have coordinate-sorted BAM files from single-cell ATAC-seq experiments (e.g., 10X Genomics scATAC-seq) and need to generate a compressed fragment file for efficient downstream analysis. Use this step before matrix generation, clustering, or peak calling in SnapATAC2.
    0 installs
92. ▌
    Boundary Detection Thresholding · holobiomicslab

    Use when when you have computed per-bin insulation scores from a Hi-C cooler file using cooltools.insulation and need to identify discrete genomic boundaries that separate topological domains.
    0 installs
93. ▌
    Dna Methylation Quality Control · holobiomicslab

    Use when immediately after loading raw .idat files or beta-value matrices from HumanMethylation450 or EPIC arrays when you need to exclude probes that fail quality control.
    0 installs
94. ▌
    Epic Array Simulation Benchmark · holobiomicslab

    Use when when developing or validating a DNA methylation array analysis pipeline using ChAMP, you need an independent ground-truth dataset to confirm that DMR detection is working correctly.
    0 installs
95. ▌
    Hi C Coverage Track Computation · holobiomicslab

    Use when you have a cooler file (.cool or .mcool) from a Hi-C experiment and need to generate a genome-wide track of per-bin sequencing depth to assess coverage uniformity, identify poorly sequenced regions, or normalize downstream analyses by local sequencing intensity.
    2 installs
96. ▌
    Hi C Expected Value Calculation · holobiomicslab

    Use when you have a cooler-format Hi-C contact matrix and need to establish a genome-wide baseline contact frequency by genomic distance.
    0 installs
97. ▌
    Kmer Annotation Matrix Assembly · holobiomicslab

    Use when you have filtered peak counts from ATAC or DNase-seq data (with GC bias correction and sample/peak filtering applied) and want to annotate peaks by k-mer content rather than known transcription factor motifs—particularly when comparing how k-mer size affects the magnitude of chromatin.
    0 installs
98. ▌
    Memory Profiling And Monitoring · holobiomicslab

    Use when when benchmarking or validating the scalability of single-cell algorithms that claim linear or sublinear space complexity, particularly when processing datasets with ≥10 million cells.
    0 installs
99. ▌
    Motif Site Occupancy Comparison · holobiomicslab

    Use when you have bias-corrected ATAC-seq footprint signals (BigWig files) from two or more distinct conditions (e.
    0 installs
100. ▌
     Python Pandas Data Manipulation · holobiomicslab

     Use when you have precomputed expected contact frequency tables (TSV format with columns like dist_bp, contact_frequency, n_valid) and need to apply log-binning and smoothing to group distance values into log-spaced bins, aggregate statistics within each bin, and export a cleaned, annotated output.
     2 installs