3版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - o删除错误时执行基于使用定义的基因集富集分析。o优先NormalizeBeta。o定制KEGG通路(04 * * *)。1.4.1版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - o优先考虑许多功能。版本1.4.0变化- - - - - - - - - - - - - - - - - - - - - - - - - o EnrichedGeneView中添加新的参数允许用户定制通路和基因。1.3.0版本版本的变化- - - - - - - - - - - - - - - - - - - - - - - - - o修复bug本质不同的有机体的基因问题。o更新EnrichedGeneView(基于adjust.pvalue排名通路)。o合并EnrichedView EnrichedGSEView,允许自定义轴。o取代EnrichGSEView enrichment_analysis的新功能。o取代旧的SquareView函数。 o Add a new function 'EnrichedFilter' to simplify enriched function terms by computing the Jaccard similarity coefficient between enriched terms, and removing big gene sets. CHANGES IN VERSION 1.2.3 ------------------------- o Prioritize FluteMLE. o Remove warnings from vignettes. CHANGES IN VERSION 1.2.2 ------------------------- o Revise ReadRRA function. o Add ReadsgRRA function to read sgrna_summary in MAGeCK RRA results. o Add sgRankView function to visualize the rank of sgRNA targeting top selected genes. o Remove bugs in FluteMLE and FluteRRA. o Add additional visualization functions in FluteRRA. o Add EnrichedGeneView to visualize the core enriched genes in enriched pathways. o Integrate WikiPathways, PID terms and EHMN pathways into enrichment functions. o Export all the hidden functions. CHANGES IN VERSION 1.2.1 ------------------------- o Add VolcanoView to show positive and negative selected genes. o Improve EnrichedView and EnrichedGSEView function. o Add QC figures in vignettes. o Merge MsigDB, KEGG, and GO genesets together and integrate them into package. CHANGES IN VERSION 1.1.6 ------------------------- o Add functions to plot figures in NatureProtocol manuscript. o Shorten the check time. o Remove null figures in pathview part. CHANGES IN VERSION 1.1.9 ------------------------- o Add parameter 'pathway_limit' / 'limit' / 'gmtpath' in FluteRRA, FluteMLE, and all enrichment functions which enable users to customize gene sets for enrichment analysis. o Remove DAVID and GOstats, which are not recommended. o Add enrichment score in enrichment results from all algorithms. CHANGES IN VERSION 1.1.1 ------------------------- o Speed up the enrichment analysis. o Release memory in time. CHANGES IN VERSION 0.99.19 ------------------------- o Beutify figures. o Remove some unnecessary dependencies. CHANGES IN VERSION 0.99.18 ------------------------- o Add HeatmapView and BatchRemove. o Change view distribution functions which show samples separately. o Change function ReadBeta to be more friendly. o Label top ten essential genes in SquareView. o Change some default parameter values to be better. CHANGES IN VERSION 0.99.10 ------------------------- o Change all plot function names ended with 'View'. o Decrease exported functions o Decrease package denpendcies o Revise all documents CHANGES IN VERSION 0.99.1 ------------------------- o Remove some new errors, such as error trigered by no GroupA genes. o Allow users to input their own essential genes to do the cell cycle normalization. o Allow users to define the number of genes labeled in rank figure, default label top 10 and bottom 10 genes. o Add annotation of other organisms. CHANGES IN VERSION 0.99.0 ------------------------- o FluteMLE and FluteRRA are two main functions in MAGeCKFlute package. FluteMLE run pipeline from gene beta scores caculated by MAGeCK MLE, while FluteRRA run pipeline based on MAGeCK RRA results.