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Gene Set Enrichment Analysis using clusterProfiler gseGO and gseKEGG. Use when analyzing ranked gene lists to find coordinated expression changes in gene sets without arbitrary significance cutoffs. Detects subtle but coordinated expression changes.

日本語の概要は準備中です。原文の説明を表示しています。

Build, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA analysis. Covers DDA-based library generation, predicted libraries (Prosit, DeepLC), and library formats.

日本語の概要は準備中です。原文の説明を表示しています。

Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).

日本語の概要は準備中です。原文の説明を表示しています。

Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.

日本語の概要は準備中です。原文の説明を表示しています。

Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.

日本語の概要は準備中です。原文の説明を表示しています。

Meta-agent that routes bioinformatics requests to specialised sub-skills. Handles file type detection, analysis planning, report generation, and reproducibility export.

日本語の概要は準備中です。原文の説明を表示しています。

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.

日本語の概要は準備中です。原文の説明を表示しています。

Post-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization, motif analysis, and quantitative PTM analysis. Use when analyzing phosphoproteomic data or other modification-enriched samples.

日本語の概要は準備中です。原文の説明を表示しています。

Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filtering by drug-likeness criteria.

日本語の概要は準備中です。原文の説明を表示しています。

Multi-Omics Factor Analysis (MOFA2) for unsupervised integration of multiple data modalities. Identifies shared and view-specific sources of variation. Use when integrating RNA-seq, proteomics, methylation, or other omics to discover latent factors driving biological variation across modalities.

日本語の概要は準備中です。原文の説明を表示しています。

Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes between experimental groups.

日本語の概要は準備中です。原文の説明を表示しています。

Detect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to identify bacterial, viral, adapter, or sample swap contamination. Use when suspecting cross-contamination or working with samples prone to microbial contamination.

日本語の概要は準備中です。原文の説明を表示しています。

Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.

日本語の概要は準備中です。原文の説明を表示しています。

All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast tool instead of separate Cutadapt, Trimmomatic, and FastQC steps.

日本語の概要は準備中です。原文の説明を表示しています。

WikiPathways enrichment using clusterProfiler and rWikiPathways. Use when analyzing gene lists against community-curated open-source pathways. Performs over-representation analysis and GSEA for 30+ species.

日本語の概要は準備中です。原文の説明を表示しています。

Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature alignment, and missing value handling across data types. Use when preparing multi-omics datasets for integration analysis.

日本語の概要は準備中です。原文の説明を表示しています。

Protein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides. Handles protein groups and protein-level FDR control using parsimony and probabilistic approaches.

日本語の概要は準備中です。原文の説明を表示しています。

Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina TruSeq, Nextera, and custom adapter sequences. Use when FastQC shows adapter contamination or before alignment of short reads.

日本語の概要は準備中です。原文の説明を表示しています。

KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.

日本語の概要は準備中です。原文の説明を表示しています。

Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.

日本語の概要は準備中です。原文の説明を表示しています。

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

日本語の概要は準備中です。原文の説明を表示しています。

Reads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure parsing, canonicalization, and full standardization pipeline including sanitization, normalization, and tautomer canonicalization. Use when loading chemical libraries, converting formats, or preparing molecules for analysis.

日本語の概要は準備中です。原文の説明を表示しています。

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

日本語の概要は準備中です。原文の説明を表示しています。

Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network. Use when performing patient stratification or integrating multi-omics data into unified similarity networks.

日本語の概要は準備中です。原文の説明を表示しています。