NEWS

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MAGeCKFlute 1.99.0

• Avoid downloading reference files
• Perform enrichment analysis based on human pathways by default

MAGeCKFlute 1.10.1

• Remove transcripts ids from uniprot data in TransGeneID
• Enable single cell type incorporation using the IncorporateDepmap

MAGeCKFlute 1.9.1

• Turn off the Depmap analysis in vignettes because it's time consuming
• Use count in EnrichedView when NES is not available

MAGeCKFlute 1.8.1

• Update the standard gene names
• Debug the color issue in the ScatterView
• Remove the usage of scale_color_npg and data.table::melt from the DensitiView
• Remove nPerm parameter from the enrich.GSE
• Download GO-gene relationship from NCBI ftp folder
• Move multiple imports to suggests
• Replace view_allpath with pathview.top in FluteMLE to allow users to set the number of pathways for pathview visualization.

MAGeCKFlute 1.7.3

• Fix the GeneRatio and BackgroundRatio issue in enrich.HGT
• Fix the pvalueCutoff issue in EnrichAnalyzer
• Remove the inpropriate description of RRA score in FACS-based screens (ReadRRA)
• Revise the pvalue to be FDR in documentations.

MAGeCKFlute 1.7.2

• Allow user customized data input.
• Prioritize the documentation.

MAGeCKFlute 1.6.4

• Config Travis CI test.
• Download Depmap data automatically and save as rdata.

MAGeCKFlute 1.6.3

• Download GO terms from source database.
• Use human genes to do enrichment analaysis in pipelines.
• Revise BatchRemove to have the same parameters as paper mentioned.
• Revise FluteRRA to surport only gene summary as input.

MAGeCKFlute 1.6.2

• Debug Depmap data loading process

MAGeCKFlute 1.6.1

• Incorporate gene id conversion between organisms into TransGeneID.
• Incorporate visualization functions from enrichplot.
• Add new functions for visualization, such as ScatterView and BarView.
• Debug the read file commands.
• Add additional document for enrichment analysis.
• Integrate Depmap data into the pipeline.

MAGeCKFlute 1.6.0

• Prioritize visualization functions in MAGeCKFlute.
• Debug FluteMLE and FluteRRA.

MAGeCKFlute 1.4.4

• Remove duplicated rows in BatchRemove results.
• Add other MsigDB genesets into MAGeCKFlute.
• Prioritize EnrichedView function.

MAGeCKFlute 1.4.3

• Remove bugs when perform enrichment analysis based on use-defined gene sets.
• Prioritize NormalizeBeta.
• Customize KEGG pathways (04***).

MAGeCKFlute 1.4.1

• Prioritize many functions.

MAGeCKFlute 1.4.0

• Add new parameters in EnrichedGeneView to allow users to customize pathways and genes to show.

MAGeCKFlute 1.3.0

• Fix the bug about essential gene issue for different organism.
• Update EnrichedGeneView (Rank pathways based on adjust.pvalue).
• Merge EnrichedView and EnrichedGSEView, which allow custom x-axis.
• Replace EnrichGSEView in enrichment_analysis by new function.
• Replace the old SquareView function.
• Add a new function 'EnrichedFilter' to simplify enriched function terms by computing the Jaccard similarity coefficient between enriched terms, and removing big gene sets.

MAGeCKFlute 1.2.3

• Prioritize FluteMLE.
• Remove warnings from vignettes.

MAGeCKFlute 1.2.2

• Revise ReadRRA function.
• Add ReadsgRRA function to read sgrna_summary in MAGeCK RRA results.
• Add sgRankView function to visualize the rank of sgRNA targeting top selected genes.
• Remove bugs in FluteMLE and FluteRRA.
• Add additional visualization functions in FluteRRA.
• Add EnrichedGeneView to visualize the core enriched genes in enriched pathways.
• Integrate WikiPathways, PID terms and EHMN pathways into enrichment functions.
• Export all the hidden functions.

MAGeCKFlute 1.2.1

• Add VolcanoView to show positive and negative selected genes.
• Improve EnrichedView and EnrichedGSEView function.
• Add QC figures in vignettes.
• Merge MsigDB, KEGG, and GO genesets together and integrate them into package.

MAGeCKFlute 1.1.9

• Add parameter 'pathway_limit' / 'limit' / 'gmtpath' in FluteRRA, FluteMLE, and all enrichment functions which enable users to customize gene sets for enrichment analysis.
• Remove DAVID and GOstats, which are not recommended.
• Add enrichment score in enrichment results from all algorithms.

MAGeCKFlute 1.1.6

• Add functions to plot figures in NatureProtocol manuscript.
• Shorten the check time.
• Remove null figures in pathview part.

MAGeCKFlute 1.1.1

• Speed up the enrichment analysis.
• Release memory in time.

MAGeCKFlute 0.99.19

• Beutify figures.
• Remove some unnecessary dependencies.

MAGeCKFlute 0.99.18

• Add HeatmapView and BatchRemove.
• Change view distribution functions which show samples separately.
• Change function ReadBeta to be more friendly.
• Label top ten essential genes in SquareView.
• Change some default parameter values to be better.

MAGeCKFlute 0.99.10

• Change all plot function names ended with 'View'.
• Decrease exported functions
• Decrease package denpendcies
• Revise all documents

MAGeCKFlute 0.99.1

• Remove some new errors, such as error trigered by no GroupA genes.
• Allow users to input their own essential genes to do the cell cycle normalization.
• Allow users to define the number of genes labeled in rank figure, default label top 10 and bottom 10 genes.
• Add annotation of other organisms.

MAGeCKFlute 0.99.0

• 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.