版本0.15-0.17（2021-12-13）的更改重大更改 - 所有富集分析均已扩展和改进，我们添加了额外的本体（KEGG，DO和Reactome），在结果的摘要图中更多信息 - 所有绘图功能 - 绘制功能都有现在可以为所有导出的图函数设置PDF宽度和高度。同样，可以不使用PDF，而是可以使用当前活动的图形设备的可能性。最后，最终可以设置不同的文件名。总体而言，这为自定义文件名，所使用的输出设备和PDF尺寸提供了最终的灵活性 - 我们添加了一个函数来构建可以参数化的EGRN网络，并且可以更轻松地进行参数化。现在，可以更改特定于网络的参数，例如是否允许循环 - 我们删除了Graniedev软件包，开发现在发生在单独的分支中而不是其他包装中 - 我们添加了Leiden Clustering以进行社区聚类（请参阅https：/ https：//www.nature.com/articles/s41598-019-41695 -Z用于与卢文的比较） - 广泛的小插图更新错误修复 - 各种较小的错误修复了较小的次要更改 - 稍微更改对象结构（统计数据中的图形插槽和结构$版本0.9-0.14（2021-12-13）的富集插槽更改 - 重大大修和对峰值基因QC图的持续工作 - FilterData函数现在具有更多的过滤参数，例如CV过滤。同样，所有过滤器都均匀地有一个分钟和最大过滤器。- 集成的网络统计和各种丰富分析 - 处理边缘案例和各种功能中的罕见事件 - 包裹已重命名为Granie为Basename（之前：GRN）错误修复 - 各种次要错误修复了次要的较小更改 - 略微更改对象结构，并移动了某些基因和峰值注释数据（例如平均值，CV）在版本0.8（2021-05-07）中的适当注释插槽变化发生了重大变化 - 改进的PCA绘图，PCA绘图现在是针对原始数据和归一化数据生成的 - 新过滤器对于功能filterGranieAndConnectgenes（peak_gene.maxDistance）以及更大的灵活性，如何调整用于多次测试的峰值原始P值（包括使用IHW的可能性 - 实验性） - 新功能PlotDienchosticplots_tfppeaks_tfppeaks以前称为绘图（此功能（此功能） only internally, but is now properly exported), in analogy to plotDiagnosticPlots_peakGene Bug fixes - various minor bug fixes (PCA plotting, compatibility when providing pre-normalized data) Minor changes - changed the object structure slightly and cleaned the config slot, for example - some functions have been added / renamed to make the workflow more clear and streamlined, see Vignette for details - some default parameters changed Changes in version 0.7 (2021-03-12) Major changes - improved PCA plotting, also works for pre-normalized counts now when provided as input originally - more flexibility for data normalization - homogenized wordings, function calls and workflow clarity, removed unnecessary warnings when plotting peak-gene diagnostic plots, added more R help documentation - added IHW (Independent Hypothesis Weighting) as a multiple testing procedure for peak-gene p-values in addition to now allowing all methods that are supported by p.adjust Bug fixes - various minor bug fixes Minor changes Changes in version 0.6 (2021-02-09) Major changes - significant speed improvements for the peak-FDR calculations and subsequent plotting - TF-peak diagnostic plots now also show negatively correlated TF-peak statistics irrespective of whether they have been filtered out in the object / pipeline. This may be useful for diagnostic purposes to check whether excluding them is a sensible choice and to confirm the numbers are low Bug fixes - Numbers for connections per correlation bin in the TF-peak diagnostic plots were wrong as they did not correctly differentiate between the different connection types in case multiple ones had been specified (e.g., expression and TF activity). This has been fixed. Minor changes Changes in version 0.5 (2021-02-02) first published package version