Data & Analytics

Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by gene/rsID/condition/review status; returns ClinSig, submitter data, conditions, HGVS. For GWAS use gwas-database; for variant consequence prediction use Ensembl VEP.

Query the ClinPGx (formerly PharmGKB) REST API plus the CPIC PostgREST companion API for pharmacogenomic clinical annotations, CPIC/DPWG dosing guidelines, gene-drug pairs, variant-drug associations, FDA/EMA drug labels, and PGx pathways. Two-host architecture: api.clinpgx.org for annotation records, api.cpicpgx.org for genotype→recommendation lookups. No auth. For germline pathogenicity use clinvar-database; for somatic cancer PGx use cosmic-database or opentargets-database; for drug bioacti...

Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use opentargets-database.

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.

Query ARCHS4 REST API for uniformly processed RNA-seq expression, tissue patterns, co-expression across 1M+ human/mouse samples. Retrieve z-scores, co-expressed genes, samples by metadata, HDF5 matrices. For variant population genetics use gnomad-database; for pathway enrichment use gget-genomic-databases (Enrichr).

Compute the bacterial pan-genome from Prokka/Bakta GFF3 annotations with Roary's CD-HIT + BLAST + MCL clustering pipeline. Builds gene presence/absence matrices, core/soft-core/shell/cloud partitions, multi-FASTA core gene alignments (with `-e`), and a pan-genome reference. Use Panaroo for higher-accuracy pan-genomes from highly fragmented assemblies, PIRATE for paralog-aware clustering, or PPanGGOLiN for graph-based partitioning.

Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.

Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.

Splice-aware RNA-seq aligner producing sorted BAM and splice junction tables. Builds genome index, runs two-pass alignment for better junctions. Outputs sorted BAM, junctions (SJ.out.tab), stats (Log.final.out), optional gene counts. Use Salmon for fast pseudoalignment; STAR when a BAM is needed for variant calling, IGV, or ENCODE pipelines.

CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.

Read/write SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ. Region queries, pileup, variant filtering, read groups. Python htslib wrapper exposing samtools/bcftools CLI. Use STAR/BWA for alignment; GATK/DeepVariant for variant calling.

Fast short-read DNA aligner for WGS/WES/ChIP-seq. 2× faster BWA-MEM successor; outputs SAM/BAM with read group headers for GATK. Primary plus supplementary records for chimeric reads. Use STAR for RNA-seq splice-aware alignment; Bowtie2 is a comparable alternative.

omics-plotting: publication-style figure authoring for omics / bioinformatics results with matplotlib / seaborn. Read this before writing any plotting or figure code in any omics analysis — RNA-seq, proteomics, single-cell, variant, or database results — not only when a plot is explicitly requested: whenever an analysis will produce a figure, load this first and follow its recipes. Covers volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA /...

Assemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from already-rendered panels the user supplies (PNG/PDF). Ask the user to pick one of two approaches: (1) redraw every panel into one unified figure using independent, tightly packed `subfigures` (each sized to its own labels, so axes need NOT align),...

3Dmol.js WebGL molecular visualization emitted as self-contained HTML. Render structures (PDB/SDF/XYZ/MOL2/cube) with stick, sphere, cartoon, line, and surface styles; animate trajectories with a frame-delay (interval, ms) control; and animate vibrational normal modes via vibrate() from per-atom dx/dy/dz displacements or from precomputed frames. Output standalone HTML that loads 3Dmol from a CDN, with optional play/pause and speed controls. Use for transition-state imaginary-mode animations, ...

Generates email reports and statistics using gog CLI. Creates daily/weekly summaries, spam stats, sender analysis, pending tasks, audit history, and exports data to Google Sheets or text files using gog sheets/docs. Use when the user wants a report, summary, statistics, or export of email activity.

Execute AetherLang V3 AI workflows from Claude Code using nine specialized engines for culinary, business, research, marketing, and strategic analyses.

Monitor new papers on arXiv by category. Use when user wants to check latest papers, track research topics, or manage reading lists. Trigger phrases: \"check arxiv\", \"new papers\", \"arxiv category\", \"watch arxiv\", \"latest papers on\".

查询指定城市或地区的天气预报信息，包括温度、天气状况、降水概率、风力风向等。支持实时天气和未来多日预报查询。

查询指定城市或地区的天气预报信息，包括温度、天气状况、降水概率、风力风向等。支持实时天气和未来多日预报查询。

Render structured table data as high-quality PNG images using Headless Chrome. Use when: need to visualize tabular data for chat interfaces, reports, or social media. NOT for: simple text tables that don't need visualization.

ChartClass

BacktestBot

Comprehensive free financial data API library — supports A-shares, Hong Kong stocks, US stocks, futures, options, funds, bonds, forex, and macro data, no API key required.