CHANGES IN VERSION 2.4.0 ------------------------- - No major changes - Small bug fixes 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