主要使用R语言编写。软件包总下载量约为10.3M，数据来自于CRAN / Bioconductor / Anaconda，更新于2026-01-27。
可视化
| Package | downloads | github | publication |
|---|---|---|---|
| circlize：圈形可视化 |  |
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| ComplexHeatmap：复杂热图可视化 |  |
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| InteractiveComplexHeatmap：交互式复杂热图 |  |
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| EnrichedHeatmap：基因组信号特定类型区间上的富集 |  |
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| HilbertCurve：希尔伯特曲线布局 |  |
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| spiralize：阿基米德螺线布局 |  |
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| gtrellis：基因组Trellis布局 |  |
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| BioCartaImage：BioCarta生物通路图像 |  |
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数据建模与分析
| Package | downloads | github | publication |
|---|---|---|---|
| sfcurve：nxn 空间填充曲线 |  |
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| simona：生物本体论（Bio-ontology）语义相似性工具箱 |  |
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| simplifyEnrichment：简化功能富集分析结果 |  |
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| cola：一致性聚类通用框架 |  |
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| rGREAT：基于基因组区间的功能富集 |  |
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| CePa：基于网络中心性的生物通路富集 |  |
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数据注释
| Package | downloads | github |
|---|---|---|
| GeneSummary：RefSeq数据库的基因概要数据 |  |
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| UniProtKeywords：UniProt数据库的关键字数据 |  |
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| BioMartGOGeneSets：来自BioMart的GO基因集合数据 |  |
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| IlluminaHumanMethylationEPICv2anno.20a1.hg38：Epic甲基化芯片v2注释数据 |  |
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| IlluminaHumanMethylationEPICv2manifest：Epic甲基化芯片v2注释数据 |  |
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实用工具
| Package | downloads | github | publication |
|---|---|---|---|
| pkgndep：依赖重量分析 |  |
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| bsub：发送R代码至LSF计算集群 |  |
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| GetoptLong：命令行参数解析 |  |
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| GlobalOptions：设定全局参数 |  |
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教学
| Package | github |
|---|---|
| GSEAtopics：基因集合富集分析若干主题 |  |
在线书籍
软件包状态
| 软件包 | CRAN check | bioc-devel | bioc-release | GitHub issues (opened) | GitHub issues (closed) |
|---|---|---|---|---|---|
| circlize |  |
- | - |  |
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| spiralize | |
- | - |  |
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| GetoptLong | |
- | - |  |
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| GlobalOptions | |
- | - |  |
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| bsub | |
- | - |  |
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| pkgndep |  |
- | - |  |
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| simona | - |  |
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| simplifyEnrichment | - |  |
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| ComplexHeatmap | - |  |
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| InteractiveComplexHeatmap | - |  |
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| EnrichedHeatmap | - |  |
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| HilbertCurve | - |  |
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| gtrellis | - |  |
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| rGREAT | - |  |
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| cola | - |  |
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| GeneSummary | - | - | - |  |
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| UniProtKeywords | - | - | - |  |
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| BioMartGOGeneSets | - | - | - |  |
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| BioCartaImage | - | - | - |  |
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| IlluminaHumanMethylationEPICv2anno.20a1.hg38 | - | - | - |  |
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| IlluminaHumanMethylationEPICv2manifest | - | - | - |  |
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