CHANGES IN VERSION 1.99.0 ------------------------- o Avoid downloading reference files o Perform enrichment analysis based on human pathways by default CHANGES IN VERSION 1.10.1 (Bioconductor 3.11) ------------------------- o Remove transcripts ids from uniprot data in TransGeneID o Enable single cell type incorporation using the IncorporateDepmap CHANGES IN VERSION 1.9.1 (Bioconductor 3.11) ------------------------- o Turn off the Depmap analysis in vignettes because it's time consuming o Use count in EnrichedView when NES is not available CHANGES IN VERSION 1.8.1 (Bioconductor 3.11) ------------------------- o Update the standard gene names o Debug the color issue in the ScatterView o Remove the usage of scale_color_npg and data.table::melt from the DensitiView o Remove nPerm parameter from the enrich.GSE o Download GO-gene relationship from NCBI ftp folder o Move multiple imports to suggests o Replace view_allpath with pathview.top in FluteMLE to allow users to set the number of pathways for pathview visualization. CHANGES IN VERSION 1.7.3 (Bioconductor 3.11) ------------------------- o Fix the GeneRatio and BackgroundRatio issue in enrich.HGT o Fix the pvalueCutoff issue in EnrichAnalyzer o Remove the inpropriate description of RRA score in FACS-based screens (ReadRRA) o Revise the pvalue to be FDR in documentations. CHANGES IN VERSION 1.7.2 (Bioconductor 3.11) ------------------------- o Allow user customized data input. o Prioritize the documentation. CHANGES IN VERSION 1.6.4 (Bioconductor 3.10) ------------------------- o Config Travis CI test. o Download Depmap data automatically and save as rdata. CHANGES IN VERSION 1.6.3 (Bioconductor 3.10) ------------------------- o Download GO terms from source database. o Use human genes to do enrichment analaysis in pipelines. o Revise BatchRemove to have the same parameters as paper mentioned. o Revise FluteRRA to surport only gene summary as input. CHANGES IN VERSION 1.6.2 (Bioconductor 3.10) ------------------------- o Debug Depmap data loading process CHANGES IN VERSION 1.6.1 (Bioconductor 3.10) ------------------------- o Incorporate gene id conversion between organisms into TransGeneID. o Incorporate visualization functions from enrichplot. o Add new functions for visualization, such as ScatterView and BarView. o Debug the read file commands. o Add additional document for enrichment analysis. o Integrate Depmap data into the pipeline. CHANGES IN VERSION 1.6.0 (Bioconductor 3.10) ------------------------- o Prioritize visualization functions in MAGeCKFlute. o Debug FluteMLE and FluteRRA. CHANGES IN VERSION 1.4.4 (Bioconductor 3.9) ------------------------- o Remove duplicated rows in BatchRemove results. o Add other MsigDB genesets into MAGeCKFlute. o Prioritize EnrichedView function. CHANGES IN VERSION 1.4.3 (Bioconductor 3.9) ------------------------- o Remove bugs when perform enrichment analysis based on use-defined gene sets. o Prioritize NormalizeBeta. o Customize KEGG pathways (04***). CHANGES IN VERSION 1.4.1 (Bioconductor 3.9) ------------------------- o Prioritize many functions. CHANGES IN VERSION 1.4.0 (Bioconductor 3.9) ------------------------- o Add new parameters in EnrichedGeneView to allow users to customize pathways and genes to show. CHANGES IN VERSION 1.3.0 (Bioconductor 3.9) ------------------------- o Fix the bug about essential gene issue for different organism. o Update EnrichedGeneView (Rank pathways based on adjust.pvalue). o Merge EnrichedView and EnrichedGSEView, which allow custom x-axis. o Replace EnrichGSEView in enrichment_analysis by new function. o Replace the old SquareView function. 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 (Bioconductor 3.9) ------------------------- o Prioritize FluteMLE. o Remove warnings from vignettes. CHANGES IN VERSION 1.2.2 (Bioconductor 3.9) ------------------------- 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 (Bioconductor 3.9) ------------------------- 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 (Bioconductor 3.9) ------------------------- 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 (Bioconductor 3.9) ------------------------- 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 (Bioconductor 3.9) ------------------------- o Speed up the enrichment analysis. o Release memory in time. CHANGES IN VERSION 0.99.19 (Bioconductor 3.9) ------------------------- o Beutify figures. o Remove some unnecessary dependencies. CHANGES IN VERSION 0.99.18 (Bioconductor 3.9) ------------------------- 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 (Bioconductor 3.9) ------------------------- 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 (Bioconductor 3.9) ------------------------- 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 (Bioconductor 3.9) ------------------------- 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.