Dados e Análise

Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for multi-DB Python SDK use bioservices.

Next.js best practices - file conventions, RSC boundaries, data patterns, async APIs, metadata, error handling, route handlers, image/font optimization, bundling

Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

Complete pre-game analysis for a single NHL (or other sport) matchup: team records, goalie matchup, key stats, odds snapshot, model edge, and head-to-head history in one shareable report. Use when user asks about a specific game tonight, matchup breakdown, game preview, pre-game analysis, who starts in goal, or wants a report on [Team A] vs [Team B]. Do not use for full slate analysis -- see daily

Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.

WSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep, tile-based DL, slide QC. Use pathml for multiplexed imaging.

Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity satu

SQL standards — UUID v7 PKs, snake_case, soft delete, forward-only migrations, parameter binding, N+1 prevention, EXPLAIN-driven indexing. PostgreSQL 18 primary; MySQL 9 and SQLite 3.53 noted. Use when designing schemas, writing queries, or auditing a database layer.

End-to-end small RNA-seq analysis from FASTQ to differential miRNA expression. Use when analyzing miRNA, piRNA, or other small RNA sequencing data.

Uma biblioteca Python para trabalhar com dados vetoriais geoespaciais como shapefiles, GeoJSON e GeoPackage. É utilizada para análise espacial, operações geométricas, transformações de coordenadas e tarefas que envolvem leitura, escrita ou análise de dados geográficos vetoriais, com suporte a bancos de dados PostGIS e mapas interativos.

Guide users through omicverse's spatial transcriptomics tutorials covering preprocessing, deconvolution, and downstream modelling workflows across Visium, Visium HD, Stereo-seq, and Slide-seq datasets.