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概要と使いどころ
Consensus cell type annotation: runs 10+ algorithms (KNN-Harmony/BBKNN/Scanorama/scVI, CellTypist, ONCLASS, Random Forest, SCANVI, SVM, XGBoost) on a labeled reference and transfers labels via majority voting. Outputs per-method labels, consensus, agreement score. Use when single-method annotation is insufficient or you need ensemble uncertainty for novel states.
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Deep generative models for single-cell omics: probabilistic batch correction (scVI), semi-supervised annotation (scANVI), CITE-seq RNA+protein (totalVI), transfer learning (scARCHES), and DE with uncertainty. Unified setup→train→extract API on AnnData. Use harmony-batch-correction for fast linear correction without deep learning; muon for multi-modal MuData workflows.
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CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.
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Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). Scores range 1a (strongest) to 7 (none). Use for GWAS hit prioritization, regulatory variant annotation, cis-regulatory discovery. Use clinvar-database for pathogenicity; gwas-database for trait associations.
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Detect somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use GATK CNV for deep WGS with population controls; use CNVkit for targeted/exome where antitarget bins matter.
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Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by species, peaks filtered by biotype (promoter, enhancer), and BED files for a TF-cell type pair. Use for TF co-occupancy, regulatory annotation, and TF binding atlases. Use jaspar-database for PWM motifs; encode-database for ENCODE tracks.
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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).
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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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Genomic interval ops on BED/BAM/GFF/VCF. Find overlaps, merge intervals, compute coverage, extract FASTA, find nearest features. Core for ChIP-seq peak annotation, region filtering, genome arithmetic. Use tabix for indexed single-region queries; use deeptools for normalized bigWig coverage.
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Python library for genomic interval ML. Train/apply region2vec embeddings turning BED regions into vectors, index interval datasets for ML, search embedding space with BEDSpace, and evaluate embedding quality. Use for chromatin accessibility clustering, regulatory element classification, and cross-sample region comparison.
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Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.
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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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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.
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Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.
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Bulk RNA-seq DE with PyDESeq2: load counts, normalize, fit negative binomial models, Wald test (BH-FDR), LFC shrinkage, volcano/MA plots. Use for two-group comparisons, multi-factor designs with batch correction, multiple contrasts.
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Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker inspection.
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Query NCBI dbSNP for SNP records by rsID, gene, or region via E-utilities and Variation Services REST API. Retrieve alleles, MAF, variant class (SNV/indel/MNV), clinical links, cross-DB IDs (ClinVar, dbVar, 1000G). Free; 3 req/sec (10 with key). For clinical pathogenicity use clinvar-database; for population frequencies use gnomad-database.
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NHGRI-EBI GWAS Catalog REST API for SNP-trait associations from published GWAS. Query studies, associations, variants, traits, genes, summary stats. Build PRS candidates, analyze pleiotropy, fetch stats for Manhattan plots. No auth.
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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.
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Counts RNA-seq reads overlapping GTF gene features. Takes sorted STAR BAMs plus GTF; outputs a per-gene tab-delimited matrix across samples. Handles strandedness (0/1/2), paired-end, multi-sample batch counting in one command, and outputs assignment statistics. Use Salmon for alignment-free quantification; use featureCounts when STAR BAMs already exist.
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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.
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NCBI GEO access via GEOparse and E-utilities. Search by keyword/organism/platform, download GSE series matrices, parse GPL annotations, extract GSM metadata, load expression matrices into pandas. For single-cell use cellxgene-census; for multi-DB access use gget-genomic-databases.
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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.
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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.
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