Changes in version 2.4.0 o No major changes o Small bug fixes Changes in version 2.2.0 o Vignette Updates o Minor bug fixes Changes in version 2.0.0 o Release of version 2.0 o Fully reworked analysis workflow for binding site definition o Additional workflow for differential binding analysis added o Enhanced options of workflow customization Changes in version 1.7.12 o Updated the vignette to feature differential binding analysis Changes in version 1.7.11 o assignToGenes() no requires binding sites to fully overlapp the gene range to be assigned to that gene o added plotBsMA() and plotBsVolcano() to visualize differential binding output Changes in version 1.7.10 o added calculateBsBackground() and calculateBsFoldChange() core function for differntial binding analysis Changes in version 1.7.9 o fixed a bug in combineBSF() where meta data was not correctly merged Changes in version 1.7.8 o added combineBSF() function to combine two or more object of type BSFDataSet Changes in version 1.7.7 o Fixed a bug in exportToBED() which caused the export to fail if the last function exectuted was calculateSignalToFlankScore() o Updated rangeCoveragePlot() to work with clipCoverage() function o Added the clipCoverage() function as improoved function calculate coverage Changes in version 1.7.6 o Update assignToGenes() to not require a gene annotation when options 'remove' or 'keep' is selected Changes in version 1.7.5 o Update vignette to include all new options o Exchanged default test object to fit new class definition o Let estimateBsWidth() fail more gracefull when no maximum can be found o Fix name space dependencies Changes in version 1.7.4 o Added region length based normalization to transcriptRegionSpectrumPlot() o Changed minWidth default from (3 -> 2) in makeBindingSites() o Allow object subsetByChr() to handle multiple chromosomes o Added calculateSignalToFlankScore() function o Added binding site definedness plot o Added a 'local' version to estimateBsWidth() if no maximum can be found on global level o Added a 'sensitivity' mode to estimateBsWidth() Changes in version 1.7.3 o Started major rework o Restructuring of class definition o Added BSFind() as core function o Added workflow functions pureClipGlobalFilter(), estimateBsWidth(), pureClipGeneWiseFilter(), assignToGenes(), assignToTranscriptRegions() o Reworked makeBindingSites(), reproducibilityFilter(), annotateWithScore() o Added plotting functions processingStepsFlowChart(), pureClipGlobalFilterPlot(), estimateBsWidthPlot(), duplicatedSitesPlot(), mergeCrosslinkDiagnosticsPlot(), makeBsSummaryPlot(), reproducibilityFilterPlot(), reproducibilitySamplesPlot(), reproducibilityScatterPlot(), geneOverlapsPlot(), targetGeneSpectrumPlot(), transcriptRegionOverlapsPlot(), transcriptRegionSpectrumPlot(), bindingSiteDefinednessPlot() Changes in version 1.7.2 o Added further input checks to reproducibilityFilter() function Changes in version 1.7.1 o Fix Namesspace issues Changes in version 1.6.1 o Fix bugs in colorPalette option o Added custom coloring Changes in version 1.5.1 o Fix Namesspace issues to prepare BioC 3.16 release Changes in version 1.4.2 o Added additional examples for multiple conditions o Added bindingSiteDetailsPlot() function Changes in version 1.4.1 o re-work of the vignette o implemented bindingSiteCoveragePlot() function o added subsetting by index functionalities o parameters minCrosslinks and minClSites can be deactivated when set to 0 o coverageOverRanges() function fails with error message on subscript out of bounds o fixed bug in ReproducibilityFilter() function o fix silent option in BSFDataSet constructor Changes in version 1.1.2 o coverageOverRanges() can be allowed to produce NAs for uneven ranges in the output Changes in version 1.1.1 o 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 o Released to Bioconductor version 3.14 Changes in version 0.99.10 o 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 o BSFDataSet() and BSFDataSetFromBigWig() now check the path to the bigwig files in the meta data for potential duplicates o coverageOverRanges() now supports also ranges with different width, if returnOption = `merge_positions_keep_replicates` o Fix bug in makeBindingSites(); The minWidth parameter is now implemented as true lower boundary (>= instead of >). The default has changed from 2 to 3. o Fix description in makeBindingSites(); The minCrosslinks parameter describes the number of positions covered by crosslink events, instead of the total number of crosslinks. o Updated color scheme in rangeCoveragePlot(); and changed position of indicator box o Updated visual of reproducibiliyCutoffPlot() function Changes in version 0.99.8 o Updated coverageOverRange(), Function now does support different output formats, summarizing the coverage differently over range, replicates and condition Changes in version 0.99.7 o Fix bugs for Bioconductor submission Changes in version 0.99.0 o --------------------------- (2021-05-15) o Submitted to Bioconductor