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.
