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概要と使いどころ
scRNA-seq with Scanpy: QC, normalization, HVG selection, PCA, neighborhood graph, UMAP/t-SNE, Leiden clustering, markers, cell annotation, trajectory inference. Standard scRNA-seq exploration.
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NGS CLI for ChIP/RNA/ATAC-seq. BAM→bigWig with RPGC/CPM/RPKM, sample correlation/PCA, heatmaps/profiles around features, fingerprints. For alignment use STAR/BWA; for peak calling use MACS2.
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Ultra-fast RNA-seq transcript/gene quantification via quasi-mapping (no BAM). Builds a k-mer index from transcriptome FASTA, quantifies in minutes. Outputs TPM/count tables (quant.sf) with optional GC- and sequence-bias correction. Integrates with tximeta/tximport for DESeq2/edgeR. Use STAR when a genome-aligned BAM is needed.
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Unified Python interface to 40+ bioinformatics web services: UniProt proteins, KEGG pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.
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Analyze MD trajectories from GROMACS, AMBER, NAMD, CHARMM, LAMMPS. Reads topology/trajectory into Universe objects; supports RMSD, RMSF, radius of gyration, contact maps, H-bonds, PCA, and custom distance/angle calculations. Use for post-simulation structural analysis; use OpenMM/GROMACS for running simulations.
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Parse local DrugBank XML for drug info, interactions, targets, and properties. Search by ID/name/CAS, extract DDIs with severity, map targets/enzymes/transporters, compute SMILES similarity. Primary via local XML; REST API rate-limited (3k/month dev). For live bioactivity use chembl-database-bioactivity; for compound properties use pubchem-compound-search.
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Molecular featurization hub (100+ featurizers) for ML. SMILES to fingerprints (ECFP, MACCS, MAP4), descriptors (RDKit 2D, Mordred), pretrained embeddings (ChemBERTa, GIN, Graphormer), pharmacophores. Scikit-learn compatible with parallelization/caching. For QSAR, virtual screening, similarity, and molecular DL.
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mdtraj molecular dynamics trajectory analysis (Python). Reads DCD/XTC/TRR/NetCDF/H5/PDB topologies and trajectories; computes RMSD vs time, radius of gyration, per-residue RMSF, residue-residue contact frequency maps, phi/psi torsions for Ramachandran plots (general + Gly/Pro), and 8-state DSSP secondary structure. Modules: trajectory I/O, geometry (distances/angles/dihedrals), structural analysis (RMSD/Rg/RMSF/SASA), contacts, hydrogen bonds, secondary structure (DSSP), NMR observables. For broader atom-selection grammar use mdanalysis-trajectory; for running MD simulations use OpenMM/GROMACS.
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Infer and visualize intercellular communication from scRNA-seq with CellChat (R). Build CellChat from Seurat/counts → subset CellChatDB ligand-receptor pairs → over-expressed genes per group → communication probabilities → pathway signaling → network centrality (senders/receivers/influencers) → chord/heatmap/bubble plots → cross-condition compare. Human, mouse. Use liana for pure-Python.
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Core Python library for astronomy/astrophysics: units with dimensional analysis, celestial coordinate transforms (ICRS/Galactic/AltAz/FK5), FITS I/O, tables (FITS/HDF5/VOTable/CSV), cosmology (Planck18, distance/age), precise time (UTC/TAI/TT/TDB, Julian, barycentric), WCS pixel-world mapping, model fitting. For general tables use pandas/polars; for radio interferometry use CASA.
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Out-of-core DataFrame for billion-row data via lazy evaluation and memory-mapped files. Use when data exceeds RAM (10 GB–TB) for fast aggregation, filtering, virtual columns, and visualization without loading. Supports HDF5, Arrow, Parquet, CSV with cloud (S3, GCS, Azure). Built-in ML transformers (scaling, PCA, K-means). In-memory: polars; distributed: dask.
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Model interpretability via SHAP (Shapley values from game theory). Covers explainer choice (Tree, Deep, Linear, Kernel, Gradient, Permutation), feature attribution, and plots (waterfall, beeswarm, bar, scatter, force, heatmap). Use to explain ML predictions, rank features, debug models, audit fairness, or compare models. Works with tree, deep, linear, and black-box models.
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Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database-access for structures.
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Low-level Python plotting for scientific figures: publication-quality line, scatter, bar, heatmap, contour, 3D; multi-panel layouts; fine control of every element. PNG/PDF/SVG export. Use seaborn for quick stats, plotly for interactive.
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Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
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Interactive scientific visualization with Plotly. Two APIs: plotly.express (px) for one-liner DataFrame plots, plotly.graph_objects (go) for trace-level control. 40+ chart types with hover, zoom, pan, animation. Exports HTML or static PNG/SVG/PDF via kaleido. Use for volcano plots with gene hover, dose-response dashboards, expression heatmaps, 3D molecular views. Use seaborn for stats; matplotlib for publication figures.
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Comprehensive best practices for robot perception systems covering cameras, LiDARs, depth sensors, IMUs, and multi-sensor setups. Use this skill when working with RGB image processing, depth maps, point clouds, sensor calibration (intrinsic, extrinsic, hand-eye), object detection, semantic segmentation, 3D reconstruction, visual servoing, or perception pipeline optimization. Trigger whenever the user mentions OpenCV, Open3D, PCL, RealSense, ZED, OAK-D, camera calibration, AprilTags, ArUco markers, stereo vision, RGBD, point cloud filtering, ICP registration, coordinate transforms, camera intrinsics, distortion correction, image undistortion, sensor streaming, frame synchronization, or any computer vision task in a robotics context. Also covers multi-camera rigs, time synchronization across sensors, perception latency budgets, and production deployment of perception pipelines.
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Provides AWS CloudFormation patterns for CloudWatch monitoring, metrics, alarms, dashboards, logs, and observability. Use when creating CloudWatch metrics, alarms, dashboards, log groups, log subscriptions, anomaly detection, synthesized canaries, Application Signals, and implementing template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references, and CloudWatch best practices for monitoring production infrastructure.
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Provides AWS CloudFormation patterns for Amazon RDS databases. Use when creating RDS instances (MySQL, PostgreSQL, Aurora), DB clusters, multi-AZ deployments, parameter groups, subnet groups, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.
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Provides AWS CloudFormation patterns for EC2 instances, Security Groups, IAM roles, and load balancers. Use when creating EC2 instances, SPOT instances, Security Groups, IAM roles for EC2, Application Load Balancers (ALB), Target Groups, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.
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Provides AWS CloudFormation patterns for Amazon S3. Use when creating S3 buckets, policies, versioning, lifecycle rules, and implementing template structure with Parameters, Outputs, Mappings, Conditions, and cross-stack references.
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Provides AWS CloudFormation patterns for DynamoDB tables, GSIs, LSIs, auto-scaling, and streams. Use when creating DynamoDB tables with CloudFormation, configuring primary keys, local/global secondary indexes, capacity modes (on-demand/provisioned), point-in-time recovery, encryption, TTL, and implementing template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references.
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Provides patterns for unit testing REST controllers using MockMvc and @WebMvcTest. Generates controller tests that validates request/response mapping, validation, exception handling, and HTTP status codes. Use when testing web layer endpoints in isolation for API endpoint testing, Spring MVC tests, mock HTTP requests, or controller layer unit tests.
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Provides AWS CloudFormation patterns for Auto Scaling including EC2, ECS, and Lambda. Use when creating Auto Scaling groups, launch configurations, launch templates, scaling policies, lifecycle hooks, and predictive scaling. Covers template structure with Parameters, Outputs, Mappings, Conditions, cross-stack references, and best practices for high availability and cost optimization.
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