
CHANGES IN VERSION 2.2.0
-------------------------

 - Vignette Updates 
 - Minor bug fixes 

CHANGES IN VERSION 2.0.0
-------------------------

 - Release of version 2.0
 - Fully reworked analysis workflow for binding site definition
 - Additional workflow for differential binding analysis added
 - Enhanced options of workflow customization


CHANGES IN VERSION 1.7.12
-------------------------

 - Updated the vignette to feature differential binding analysis

CHANGES IN VERSION 1.7.11
-------------------------

 - assignToGenes() no requires binding sites to fully overlapp the gene range to be
 assigned to that gene
 - added plotBsMA() and plotBsVolcano() to visualize differential binding output

 CHANGES IN VERSION 1.7.10
--------------------------

 - added calculateBsBackground() and calculateBsFoldChange() core function for
 differntial binding analysis


  CHANGES IN VERSION 1.7.9
--------------------------

 - fixed a bug in combineBSF() where meta data was not correctly merged

  CHANGES IN VERSION 1.7.8
--------------------------

 - added combineBSF() function to combine two or more object of type BSFDataSet

  CHANGES IN VERSION 1.7.7
--------------------------

 - Fixed a bug in exportToBED() which caused the export to fail if the last function
 exectuted was calculateSignalToFlankScore()
 - Updated rangeCoveragePlot() to work with clipCoverage() function
 - Added the clipCoverage() function as improoved function calculate coverage

  CHANGES IN VERSION 1.7.6
--------------------------

 - Update assignToGenes() to not require a gene annotation when options 'remove'
 or 'keep' is selected

  CHANGES IN VERSION 1.7.5
--------------------------

 - Update vignette to include all new options
 - Exchanged default test object to fit new class definition
 - Let estimateBsWidth() fail more gracefull when no maximum can be found
 - Fix name space dependencies

  CHANGES IN VERSION 1.7.4
--------------------------

 - Added region length based normalization to transcriptRegionSpectrumPlot()
 - Changed minWidth default from (3 -> 2) in makeBindingSites()
 - Allow object subsetByChr() to handle multiple chromosomes
 - Added calculateSignalToFlankScore() function
 - Added binding site definedness plot
 - Added a 'local' version to estimateBsWidth() if no maximum can be found on
 global level
 - Added a 'sensitivity' mode to estimateBsWidth()

  CHANGES IN VERSION 1.7.3
--------------------------

 - Started major rework
 - Restructuring of class definition
 - Added BSFind() as core function
 - Added workflow functions pureClipGlobalFilter(), estimateBsWidth(),
 pureClipGeneWiseFilter(), assignToGenes(), assignToTranscriptRegions()
 - Reworked makeBindingSites(), reproducibilityFilter(), annotateWithScore()
 - Added plotting functions processingStepsFlowChart(), pureClipGlobalFilterPlot(),
 estimateBsWidthPlot(), duplicatedSitesPlot(), mergeCrosslinkDiagnosticsPlot(),
 makeBsSummaryPlot(), reproducibilityFilterPlot(), reproducibilitySamplesPlot(),
 reproducibilityScatterPlot(), geneOverlapsPlot(), targetGeneSpectrumPlot(),
 transcriptRegionOverlapsPlot(), transcriptRegionSpectrumPlot(),
 bindingSiteDefinednessPlot()

  CHANGES IN VERSION 1.7.2
--------------------------

 - Added further input checks to reproducibilityFilter() function

  CHANGES IN VERSION 1.7.1
--------------------------

 - Fix Namesspace issues


  CHANGES IN VERSION 1.6.1
--------------------------

 - Fix bugs in colorPalette option
 - Added custom coloring

  CHANGES IN VERSION 1.5.1
--------------------------

 - Fix Namesspace issues to prepare BioC 3.16 release

  CHANGES IN VERSION 1.4.2
--------------------------

 - Added additional examples for multiple conditions
 - Added bindingSiteDetailsPlot() function

  CHANGES IN VERSION 1.4.1
--------------------------
 - re-work of the vignette
 - implemented bindingSiteCoveragePlot() function
 - added subsetting by index functionalities
 - parameters minCrosslinks and minClSites can be deactivated when set to 0
 - coverageOverRanges() function fails with error message on subscript out of
bounds
 - fixed bug in ReproducibilityFilter() function
 - fix silent option in BSFDataSet constructor

  CHANGES IN VERSION 1.1.2
--------------------------
 - coverageOverRanges() can be allowed to produce NAs for uneven ranges in the
output

  CHANGES IN VERSION 1.1.1
--------------------------
 - coverageOverRanges() matches the order of input ranges and output matrix for
options merge_all_replicates and merge_replicates_per_condition

  CHANGES IN VERSION 1.0.0
--------------------------
 - Released to Bioconductor version 3.14

  CHANGES IN VERSION 0.99.10
----------------------------
 - coverageOverRanges() now supports mean and sum as combination method. Dpending
on the returnOption, mean/ sum are computed over ranges or replicates.

  CHANGES IN VERSION 0.99.9
---------------------------
 - BSFDataSet() and BSFDataSetFromBigWig() now check the path to the bigwig
files in the meta data for potential duplicates
 - coverageOverRanges() now supports also ranges with different width, if
returnOption = `merge_positions_keep_replicates`
 - Fix bug in makeBindingSites(); The minWidth parameter is now implemented as
true lower boundary (>= instead of >). The default has changed from 2 to 3.
 - Fix description in makeBindingSites(); The minCrosslinks parameter describes
the number of positions covered by crosslink events, instead of the total
number of crosslinks.
 - Updated color scheme in rangeCoveragePlot(); and changed position of indicator
box
 - Updated visual of reproducibiliyCutoffPlot() function

  CHANGES IN VERSION 0.99.8
---------------------------
 - Updated coverageOverRange(), Function now does support different output
formats, summarizing the coverage differently over range, replicates and
condition

  CHANGES IN VERSION 0.99.7
---------------------------
 - Fix bugs for Bioconductor submission

  CHANGES IN VERSION 0.99.0
--------------------------- (2021-05-15)
 - Submitted to Bioconductor
