Web & Frontend

holobiomicslab Skill

Use when you have overlapped peak regions in GC-MS chromatography data (multiple components eluting within the same retention time window) and need to recover the pure mass spectra of each component and their relative concentrations.

holobiomicslab Skill

Use when when GC-MS chromatograms contain overlapped or co-eluting peaks in a retention time region and you need to recover the individual pure mass spectra and relative abundances of each component without manual peak picking or external standards.

holobiomicslab Skill

Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON objects, TSV match tables) that need to be reconciled into a single normalized schema for downstream aggregation.

holobiomicslab Skill

Use when you are attempting to run a web application (such as COLMARvista) locally by opening index.html directly in a browser, the application uses WebWorker and/or WebAssembly components, and these fail to load due to default file-access policies.

holobiomicslab Skill

Use when after computeDeviations has generated a SummarizedExperiment object with z-score assays reflecting bias-corrected deviations of observed vs. expected accessibility at motif or kmer sites.

holobiomicslab Skill

Use when when you need to reproduce or validate benchmark comparisons between clustering methods on single-cell chromatin accessibility data, particularly when the source publication reports multiple accuracy metrics across heterogeneous datasets and you must decide which method variant (e.

holobiomicslab Skill

Use when you need to reverse-engineer or document the architecture of a multi-component research software system where design information is embedded in repository structure, README declarations, setup files, or module docstrings rather than in a separate design document.

holobiomicslab Skill

Use when when you have aligned ATAC-seq BAM files and need to quantify Tn5 transposase insertion patterns around specific genomic coordinates (motif sites, peaks, regulatory regions) to detect transcription factor occupancy footprints or compare chromatin accessibility between bound and unbound.

holobiomicslab Skill

Use when you have a backed AnnData object populated with fragment coordinates (stored in .obsm['fragment_paired'] or .

holobiomicslab Skill

Use when when you have aligned paired scATAC-seq and scRNA-seq data from the same cells (multiome data) and need to create a single reduced-dimension coordinate space that integrates both chromatin accessibility and gene expression signals for joint clustering, trajectory analysis, or visualization.

holobiomicslab Skill

Use when when training a multi-component deep learning model where some components (e.g., a pretrained TCN spectrum encoder) should remain frozen while others (e.

holobiomicslab Skill

Use when after computing expected accessibility from filtered peak and sample counts, and before computing final deviation scores. Use this skill when working with sparse ATAC-seq or DNase-seq data where GC bias and accessibility depth are known confounders of motif-associated variability.

holobiomicslab Skill

Use when you have loaded raw ATAC-seq fragment counts into a SummarizedExperiment object and are preparing to compute motif deviations.

holobiomicslab Skill

Use when after you have (1) corrected ATAC-seq BAM files for Tn5 insertion bias using ATACorrect, (2) computed per-base footprint scores using ScoreBigwig, (3) obtained a motif database (e.

holobiomicslab Skill

Use when after completing batch normalization and quality control filtering on a Metaboprep object, when you need to communicate QC decisions, visualize exclusion patterns, and export final processed data for downstream analysis or sharing with collaborators.

holobiomicslab Skill

Use when you have raw GC-MS output in CSV format (with Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, and File.Name columns) and need to systematically rank putative identifications by match quality and exact mass agreement.

holobiomicslab Skill

Use when you have a GNPS GraphML molecular network and need to isolate cohesive subsets of spectra (components) before analyzing which fragmentation patterns explain them.

holobiomicslab Skill

Use when when you have filtered ATAC-seq or DNAse-seq peak counts (after GC bias correction, sample filtering, and peak filtering) and wish to measure how strongly each annotation (motif or kmer) influences chromatin accessibility variability in each sample relative to a background expectation.

holobiomicslab Skill

Use when you are building or extending a multi-module Python library for scientific computation (e.

holobiomicslab Skill

Use when use this skill after performing Tn5 bias correction and footprint scoring on ATAC-seq BAM files when you need to inspect the spatial distribution of Tn5 insertions around transcription factor binding sites, validate footprinting quality, or communicate differential TF occupancy patterns.

holobiomicslab Skill

Use when you have filtered peak or chromatin accessibility counts and need to annotate each peak with the presence or absence of specific DNA sequence patterns—either predefined motifs (e.

holobiomicslab Skill

Use when you have a GC-MS dataset in CSV format with retention times, base peak m/z values, component areas, and compound names, and you need to identify whether specific query chemicals are present in your samples and retrieve their -match factors (scoring the confidence of the spectral match) and.

holobiomicslab Skill

Use when when your metadata table contains species, genus, or family names that may be outdated, synonymous, or non-canonical, and you need to integrate them with the Literature Component (which requires standardized taxon identifiers) or cross-reference with external databases like Lotus Database.

holobiomicslab Skill

Use when after GCMSFormer (or similar Transformer model) has predicted pure mass spectra (matrix S) for all components in overlapped GC-MS peaks, apply this skill to quantify the relative abundance of each component.

holobiomicslab Skill

Use when you have a preprocessed GC-MS dataset (from spreadOut) with standardized column names (Compound.Name, Component.RT, Base.Peak.MZ, Component.Area, Match.Factor) and a specific list of chemical compounds you want to extract and aggregate across multiple sample runs.

holobiomicslab Skill

Use when you have raw GC-MS output in CSV format (with columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.

holobiomicslab Skill

Use when you have completed independent batch searches across one or more domain-specific MASST tools (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and received multiple separate output files (_microbe.html, _plant.json, _matches.tsv, _library.tsv, _datasets.tsv, _count_domain.

holobiomicslab Skill

Use when after installing ENPKG or any component of the workflow via conda/pip dependency manifests and before executing workflow scripts.

holobiomicslab Skill

Use when after training a multi-component neural network architecture (e.

holobiomicslab Skill

Use when after merging methylation call files from multiple samples using unite() to create a methylBase object, apply PCA when you need to visualize sample-level relationships based on overall methylation similarity across all covered bases, or when you want to determine which principal components.

holobiomicslab Skill

Use when your mass spectrometry DataFrame contains m/z, retention time (or mobility), and intensity columns, and you need to generate an interactive HTML figure for exploration, web-based presentation, or interactive supplementary material.

holobiomicslab Skill

Use when you have raw GCxGC-MS chromatogram data in NetCDF format from multiple samples (e.g., case and control groups) and need to prepare them for multivariate analysis such as multiway principal component analysis (MPCA).

holobiomicslab Skill

Use when after generateComponents has assigned candidate TP features to parent features and computed similarity metrics (spectrum similarity, fragment matches, neutral loss matches, retention time differences), use this skill to narrow the candidate pool to high-confidence parent–TP pairs that.

holobiomicslab Skill

Use when you have filtered ATAC-seq peak counts, matched motifs to those peaks, and want to measure which transcription factor motifs show elevated or reduced accessibility relative to GC-content and accessibility-matched background expectations—particularly when annotating TF motif usage across.

holobiomicslab Skill

Use when you have access to a multi-component research software repository (e.

holobiomicslab Skill

Use when when compiling or maintaining a catalog of web-accessible scientific tools (e.