NEWS

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BindingSiteFinder 2.4.0

• No major changes
• Small bug fixes

BindingSiteFinder 2.2.0

• Vignette Updates
• Minor bug fixes

BindingSiteFinder 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

BindingSiteFinder 1.7.12

• Updated the vignette to feature differential binding analysis

BindingSiteFinder 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

BindingSiteFinder 1.7.10

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

BindingSiteFinder 1.7.9

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

BindingSiteFinder 1.7.8

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

BindingSiteFinder 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

BindingSiteFinder 1.7.6

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

BindingSiteFinder 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

BindingSiteFinder 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()

BindingSiteFinder 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()

BindingSiteFinder 1.7.2

• Added further input checks to reproducibilityFilter() function

BindingSiteFinder 1.7.1

• Fix Namesspace issues

BindingSiteFinder 1.6.1

• Fix bugs in colorPalette option
• Added custom coloring

BindingSiteFinder 1.5.1

• Fix Namesspace issues to prepare BioC 3.16 release

BindingSiteFinder 1.4.2

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

BindingSiteFinder 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

BindingSiteFinder 1.1.2

• coverageOverRanges() can be allowed to produce NAs for uneven ranges in the output

BindingSiteFinder 1.1.1

• coverageOverRanges() matches the order of input ranges and output matrix for options merge_all_replicates and merge_replicates_per_condition

BindingSiteFinder 1.0.0

• Released to Bioconductor version 3.14

BindingSiteFinder 0.99.10

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

BindingSiteFinder 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

BindingSiteFinder 0.99.8

• Updated coverageOverRange(), Function now does support different output formats, summarizing the coverage differently over range, replicates and condition

BindingSiteFinder 0.99.7

• Fix bugs for Bioconductor submission

BindingSiteFinder 0.99.0

• ————————— (2021-05-15)
• Submitted to Bioconductor