修改版本2.20.0 ------------------------- o新函数' import '导入结果从差异表达分析与limma, edgeR，和DESeq2 o新函数' showAvailableCollections '列出支持的物种的基因集数据库的选择(GO, KEGG, MSigDB，富贵，…)o新函数' showAvailableCollections '列出支持的物种的基因集数据库的选择(GO, KEGG, MSigDB，富贵，…)o基因集:获取和缓存不同基因ID类型的基因集。type ' for function ' getGenesets ') o GO基因集:通过GO证据代码过滤(新参数' evid ' for function ' getGenesets ') o在nbea方法中包括NEAT方法。支持额外的基因集数据库- getGenesets(db = "msigdb")从msigdb中获得11个不同物种的基因集(通过msigdbr) - getGenesets(db = " enrichment ")从enrichment中获得5个不同物种的基因集库o基因集和基因调控网络的基因ID映射(函数' idMap ') o实现RNA-seq数据的方差稳定转换(函数' normalize '与参数' norm。方法= "vst" ')来简化遗留丰富方法的应用CHANGES IN VERSION 2.12.0 ------------------------- o对summarizeexperiment的行名的ID映射的主要重构:(函数idMap / probe2gene): - to。ID也可以是rowData列，以支持用户定义的映射-支持多:1和1:多映射的数据驱动策略-微阵列探针ID映射(probe2gene)和通用基因ID映射(idMap)的同步行为o基于GSEABase::GeneSet和GSEABase::GeneSetCollection的基因集的替代表示，以促进基因集的基因ID映射(函数getGenesets) o HTML报告的输出目标(函数eaBrowse / ebrowser):通过参数输出扩展控制。o DE和EA结果表中名义和调整后的p值的分离(函数deAna / sbea / nbea) CHANGES in VERSION 2.10.0 ------------------------- o添加脚本到inst/scripts以从命令行调用富贵浏览器(对于非r用户)o GRN编译:支持额外的路径数据库(通过graphite) o缓存下载GO和KEGG基因集(通过BiocFileCache) o默认输出目的地更改为rappdirs::user_data_dir(“mentbrowser”)o函数名称:x.x标记的废弃- read.eset -> readSE - probe.2.gene.eset -> probe2gene - de.ana -> deAna - compileGRN .from. KEGG -> compileGRN - ggea。graph -> ggeaGraph - make.example.data -> makeExampleData CHANGES IN VERSION 2.8.0 ------------------------ o从ExpressionSet到summarizeexperiment CHANGES IN VERSION 2.4.0 ------------------------ o添加了一个min.cpm过滤器用于RNA-seq数据到de.ana o额外的sbea方法:gsa, mgsa, padog, globaltest, roast, camera, gsa o额外的nbea方法:Netgsa, degraph, topologygsa, ganpa， cepa CHANGES IN VERSION 2.2.0 ------------------------- o Slight modification on ORA's hypergeometric p-value calculation according to http://mengnote.blogspot.de/2012/12/calculate-correct-hypergeometric-p.html o Adapting GGEA to also deal with 2-column GRNs o Adapting SPIA to deal with non-kegg gene sets o Including EmpiricalBrownsMethod (ebm) among sbea methods CHANGES IN VERSION 2.0.0 ------------------------- o major overhaul of the look'n'feel based on ReportingTools o interactive graphics using imageMap o reworked set and graph view o new kegg view based on pathview o adaption of specific local statistics for RNA-seq data for sample-permutation methods GSEA, SAFE, and SAMGS o Including PathNet among nbea methods o GSEA permutation approximation based on npGSEA o extended combination functionality CHANGES IN VERSION 1.2.0 ------------------------ o de.ana: extensions for RNA-seq now includes DESeq and edgeR o get.go.genesets: new getter for GO genesets o de.ana: now based on limma functionality o ggea.graph: extended control of layout o ggea: * permutation p-value now based on fast edge resampling * p-value approximation now based on gaussian mixture * extended control for edge selection (consistency threshold, edge type, ...) CHANGES IN VERSION 1.0.0 ------------------------ o Initial release of the 'EnrichmentBrowser' package