Capabilities

能力目录 (Capabilities)

Linxira Bio SDK 以 <domain>.<verb>.v1 版本化能力契约为唯一语义契约,贯穿 CLI、worker、MCP、GUI 与 SDK。当前目录共 115 项能力:112 可用 (available)、2 计划中 (planned)、1 实验性 (experimental)。

计划中的能力(protein.af2.predict.v1、protein.af3.server.v1)不可调用;实验性能力(system.gui.v1)仅限桌面应用。

system (3)

• system.doctor.v1 — linxira-bio doctor --json
• system.worker.v1 — worker 作业执行
• system.gui.v1 (experimental) — 桌面应用

environment (3)

• environment.audit.v1 — linxira-bio environment audit --json
• environment.plan.v1 — linxira-bio environment plan [PROFILE] [--mode MODE] ...
• environment.apply.v1 (planned) — 安装执行;保持规划,不可执行

runtime (1)

• runtime.catalog.v1 — linxira-bio runtime catalog --json

sequence (15)

• sequence.stats.v1 — FASTA/装配统计
• sequence.extract.v1 — 按 ID/区间提取
• sequence.filter.v1 — 长度/GC/N 过滤
• sequence.reverse-complement.v1
• sequence.translate.v1
• sequence.orf.v1
• sequence.id.normalize.v1
• sequence.merge.v1
• sequence.split.v1
• sequence.to-table.v1 / sequence.from-table.v1
• sequence.kmer.count.v1
• sequence.consensus.v1
• sequence.shuffle.v1
• sequence.convert.biopython.v1 — Biopython 格式转换包

primer (1)

• primer.epcr.v1 — 电子 PCR

dataset (1)

• dataset.inspect.v1 — 数据识别/校验/安全预览

table (2)

• table.export.v1 — 导出 CSV/TSV/JSON/JSONL/XLSX
• table.manipulate.v1 — 筛选/整形/导出

annotation (8)

• annotation.gxf.stats.v1 / annotation.gxf.normalize.v1 / annotation.gene-position.v1 / annotation.gxf.to-bed.v1 / annotation.sequence.extract.v1 / annotation.structure.visualize.v1 / annotation.go.normalize.v1 / annotation.eggnog.normalize.v1

genome (1)

• genome.gene-density.v1

fastq (5)

• fastq.qc.v1 / fastq.trim.v1 / fastq.adapter.v1 / fastq.deduplicate.v1 / fastq.subsample.v1

interval (4)

• interval.intersect.v1 / interval.merge.v1 / interval.subtract.v1 / interval.closest.v1

alignment (6)

• alignment.qc.v1 (SAM 文本) / alignment.bam-cram.qc.v1 / alignment.coverage.v1 / alignment.bam-to-bigwig.v1 / alignment.short-read.v1 / alignment.long-read.v1

variant (6)

• variant.stats.v1 / variant.compare.v1 / variant.filter.v1 / variant.normalize.v1 / variant.to-table.v1 / variant.annotate.v1

structure (7)

• structure.pdb.summary.v1 (含 AlphaFold pLDDT) / structure.viewer.v1 / structure.mmcif.summary.v1 / structure.sequence.extract.v1 / structure.contact-map.v1 / structure.geometry.v1 / structure.superpose.v1

expression (8)

• expression.differential.v1 (DESeq2 包) / expression.matrix.qc.v1 / expression.normalize.v1 / expression.pca.v1 / expression.cluster.v1 / expression.heatmap.v1 / expression.volcano.v1 / expression.wgcna.v1

set (2)

• set.venn.v1 / set.upset.v1

protein (6)

• protein.properties.v1 / protein.domain.parse.v1 / protein.domain.visualize.v1 / protein.secondary-structure.v1 / protein.af2.predict.v1 (planned) / protein.af3.server.v1 (planned)

similarity (5)

• similarity.blast.parse.v1 / similarity.blast.local.v1 / similarity.diamond.v1 / similarity.hmmer.v1 / similarity.reciprocal.v1

phylogeny (4)

• phylogeny.tree.transform.v1 / phylogeny.distance.v1 / phylogeny.iqtree.v1 / phylogeny.tree.visualize.v1

msa (2)

• msa.muscle.v1 / msa.trimal.v1

motif (3)

• motif.meme.v1 / motif.visualize.v1 / motif.mast.v1

enrichment (5)

• enrichment.overrepresentation.v1 / enrichment.go.v1 / enrichment.kegg.v1 / enrichment.gsea.v1 / enrichment.visualize.v1

medical (10, 研究用途)

• medical.cohort-table.qc.v1 / medical.bulk-rnaseq.v1 / medical.pathway-ruo.v1 / medical.variant-cohort.v1 / medical.single-cell-qc.v1
• medical.pharmacogenomics.v1 — PGx 星号等位基因解读 (GRCh38 离线表)
• medical.spatial-transcriptomics.v1 — 10x 稀疏矩阵汇总
• medical.microbiome.v1 — Kraken2 + α 多样性
• medical.survival.v1 — Cox 比例风险模型 (R 包)
• medical.metabolomics.v1 — mzML 质谱峰值检测

comparative (4)

• comparative.mcscanx.v1 / comparative.kaks.v1 / comparative.synteny.visualize.v1 / comparative.dotplot.v1

rna (1)

• rna.secondary-structure.v1

metagenomics (1)

• metagenomics.classify.v1 — Kraken2 分类与丰度表

chemistry (1)

• chemistry.descriptors.v1 — RDKit 理化描述符 (SDF→TSV)

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完整命令用法见 CLI-Reference;每项能力的双语详细文档位于仓库 docs/capabilities/<id>/{en-US,zh-CN}.md。