sanand0-scientific-research

Plugin sanand0-scientific-research from marketplace cascade-data-analytics in joshuarweaver/cascade-data-analytics. Commands read from the repo's manifest — 1 month ago.

Skills (118)

• aeon

  This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorit

• alphafold-database

  Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

• anndata

  This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data,

• arboreto

  Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed comp

• astropy

  Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use

• benchling-integration

  Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.

• biomni

  Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GW

• biopython

  Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

• biorxiv-database

  Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.

• bioservices

  Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).

• cellxgene-census

  Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.

• chembl-database

  Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.

• clinicaltrials-database

  Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.

• clinpgx-database

  Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.

• clinvar-database

  Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.

• cobrapy

  Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

• cosmic-database

  Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.

• dask

  Parallel/distributed computing. Scale pandas/NumPy beyond memory, parallel DataFrames/Arrays, multi-file processing, task graphs, for larger-than-RAM datasets and parallel workflows.

• datacommons-client

  Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for queryi

• datamol

  Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom para

• deepchem

  Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.

• deeptools

  NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.

• denario

  Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches,

• diffdock

  Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

• dnanexus-integration

  DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.

• docx

  Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.

• pdf

  PDF manipulation toolkit. Extract text/tables, create PDFs, merge/split, fill forms, for programmatic document processing and analysis.

• pptx

  Presentation toolkit (.pptx). Create/edit slides, layouts, content, speaker notes, comments, for programmatic presentation creation and modification.

• xlsx

  Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.

• drugbank-database

  Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-dr

• ena-database

  Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.

• ensembl-database

  Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.

• esm

  Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; desig

• etetoolkit

  Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

• exploratory-data-analysis

  Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown rep

• fda-database

  Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.

• flowio

  Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.

• fluidsim

  Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods

• gene-database

  Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.

• geniml

  This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to

• geo-database

  Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.

• get-available-resources

  This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions s

• gget

  CLI/Python toolkit for rapid bioinformatics queries. Preferred for quick BLAST searches. Access to 20+ databases: gene info (Ensembl/UniProt), AlphaFold, ARCHS4, Enrichr, OpenTargets, COSMIC, genome downloads. For advanced BLAST/batch processing, use biopython. For multi-database integration, use bi

• gtars

  High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.

• gwas-database

  Query NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs ID, disease/trait, gene, retrieve p-values and summary statistics, for genetic epidemiology and polygenic risk scores.

• histolab

  Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for

• hmdb-database

  Access Human Metabolome Database (220K+ metabolites). Search by name/ID/structure, retrieve chemical properties, biomarker data, NMR/MS spectra, pathways, for metabolomics and identification.

• hypogenic

  Automated hypothesis generation and testing using large language models. Use this skill when generating scientific hypotheses from datasets, combining literature insights with empirical data, testing hypotheses against observational data, or conducting systematic hypothesis exploration for research

• hypothesis-generation

  Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.

• kegg-database

  Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices. Use this for direct HTTP/REST work or KEGG-specific control.

• labarchive-integration

  Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.

• lamindb

  This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spatial, flow cytometry, etc.), tracking computational workflows, curating and validating dat

• latchbio-integration

  Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

• literature-review

  Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical,

• markitdown

  Convert various file formats (PDF, Office documents, images, audio, web content, structured data) to Markdown optimized for LLM processing. Use when converting documents to markdown, extracting text from PDFs/Office files, transcribing audio, performing OCR on images, extracting YouTube transcripts,

• matchms

  Mass spectrometry analysis. Process mzML/MGF/MSP, spectral similarity (cosine, modified cosine), metadata harmonization, compound ID, for metabolomics and MS data processing.

• matplotlib

  Foundational plotting library. Create line plots, scatter, bar, histograms, heatmaps, 3D, subplots, export PNG/PDF/SVG, for scientific visualization and publication figures.

• medchem

  Medicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS filters, structural alerts, complexity metrics, for compound prioritization and library filtering.

• metabolomics-workbench-database

  Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

• modal

  Run Python code in the cloud with serverless containers, GPUs, and autoscaling. Use when deploying ML models, running batch processing jobs, scheduling compute-intensive tasks, or serving APIs that require GPU acceleration or dynamic scaling.

• molfeat

  Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.

• networkx

  Comprehensive toolkit for creating, analyzing, and visualizing complex networks and graphs in Python. Use when working with network/graph data structures, analyzing relationships between entities, computing graph algorithms (shortest paths, centrality, clustering), detecting communities, generating

• neurokit2

  Comprehensive biosignal processing toolkit for analyzing physiological data including ECG, EEG, EDA, RSP, PPG, EMG, and EOG signals. Use this skill when processing cardiovascular signals, brain activity, electrodermal responses, respiratory patterns, muscle activity, or eye movements. Applicable for

• omero-integration

  Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

• opentargets-database

  Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

• opentrons-integration

  Lab automation platform for Flex/OT-2 robots. Write Protocol API v2 protocols, liquid handling, hardware modules (heater-shaker, thermocycler), labware management, for automated pipetting workflows.

• paper-2-web

  This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, cr

• pathml

  Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construc

• pdb-database

  Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.

• peer-review

  Systematic peer review toolkit. Evaluate methodology, statistics, design, reproducibility, ethics, figure integrity, reporting standards, for manuscript and grant review across disciplines.

• perplexity-search

  Perform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter. This skill should be used when conducting web searches for current information, finding recent scientific literature, getting grounded answers with source citations, or accessing informatio

• polars

  Fast DataFrame library (Apache Arrow). Select, filter, group_by, joins, lazy evaluation, CSV/Parquet I/O, expression API, for high-performance data analysis workflows.

• protocolsio-integration

  Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integr

• pubchem-database

  Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.

• pubmed-database

  Direct REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management. For Python workflows, prefer biopython (Bio.Entrez). Use this for direct HTTP/REST work or custom API implementations.

• pufferlib

  This skill should be used when working with reinforcement learning tasks including high-performance RL training, custom environment development, vectorized parallel simulation, multi-agent systems, or integration with existing RL environments (Gymnasium, PettingZoo, Atari, Procgen, etc.). Use this s

• pydeseq2

  Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

• pydicom

  Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM m

• pyhealth

  Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, ND

• pylabrobot

  Laboratory automation toolkit for controlling liquid handlers, plate readers, pumps, heater shakers, incubators, centrifuges, and analytical equipment. Use this skill when automating laboratory workflows, programming liquid handling robots (Hamilton STAR, Opentrons OT-2, Tecan EVO), integrating lab

• pymatgen
• pymc
• pymoo
• pyopenms
• pysam
• pytdc
• pytorch-lightning
• rdkit
• reactome-database
• reportlab
• scanpy
• scholar-evaluation
• scientific-brainstorming
• scientific-critical-thinking
• scientific-visualization
• scientific-writing
• scikit-bio
• scikit-learn
• scikit-survival
• scvi-tools
• seaborn
• shap
• simpy
• stable-baselines3
• statistical-analysis
• statsmodels
• string-database
• sympy
• tooluniverse
• torch_geometric
• torchdrug
• transformers
• umap-learn
• uniprot-database
• uspto-database
• vaex
• zarr-python
• zinc-database

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