Changes in version 1.18.0 o Deprecated the type= argument in normOffsets(). o Removed the deprecated consolidateSizes() function. o Deprecated the use of BPPARAM= in readParam(). Added the BPPARAM= argument to all relevant functions. o Modified csawUsersGuide() to point to the workflow package. Changes in version 1.16.0 o Added normFactors() function to avoid confusion when normOffsets() returns factors. o Deprecated type="scaling" option in normOffsets(). o Added calculateCPM() function for convenient calculation of (log-)CPMs. o Split up consolidateSizes() function into consolidateWindows(), consolidateTests() and consolidateOverlaps(). Deprecated consolidateSizes() itself. o Switched output of combineTests() and getBestTest() and related functions to a DataFrame. o Modified mergeWindows() behaviour with specified sign=, for dealing with nested windows of opposing sign. o Altered controlClusterFDR() to take the largest adjusted p-value threshold that yields a cluster-level FDR below target=. o Simplified detailRanges() output so that it no longer returns an arbitrary exon number. Changes in version 1.14.0 o Fully removed support for paramList objects. o Removed support for normalize(), modified default option for se.out= in normOffsert(). Changes in version 1.12.0 o Removed support for paramList objects. o Added option for normOffsets() to return SummarizedExperiment objects containing normalization data. o Deprecated normalize() to avoid S4 method clashes. o Moved scaling prior to control-based filtering into a new function, scaleControlFilter(), for greater modularity. o Updated user's guide. Changes in version 1.10.0 o Added calculation of dominant directionality in combineTests(). Fixed out-of-array indexing bug in the C++ code. o Supported factor input for ids argument in combineTests(), getBestTest(). o Added the empiricalFDR(), empiricalOverlaps() functions for controlling the empirical FDR. o Added the mixedClusters(), mixedOverlaps() functions for testing for mixed clusters. o Ensured that window-level FDR threshold chosen by controlClusterFDR() is not above the cluster-level FDR. o Minor fix to scaledAverage() to avoid slightly inaccurate results. Also, zero or negative scale factors now return -Inf and NA, respectively. o Switched to new scaleOffset() function for adding offsets in asDGEList(). Added option to specify the assay to be used. o Added multi-TSS support in detailRanges(). o Modified paired-end machinery in windowCounts(), getPESizes() to be more accommodating of overruns. o Ignored secondary and supplementary alignments in all functions. o Added options to specify assay in SE objects in filterWindows(). o Replaced weighting with normalization options in profileSites(). o Updated user's guide. Changes in version 1.8.0 o Added protection against NA values in filterWindows(). o Deprecated the use of parameter lists in any param= arguments. o Tightened up allowable values of ext= arguments in various functions. o Added the BPPARAM slot in the readParam class to store BiocParallelParam objects. o Added support for parallelization in windowCounts(), regionCounts() and others. o Updated documentation, user's guide. Changes in version 1.6.0 o Restored normalize() as a S4 method returning a RangedSummarizedExperiment object. o Modified asDGEList() to use any available normalization data in the input object. o Generalized S4 methods to apply on SummarizedExperiment objects. o Removed the rescue.ext option for PE handling, to maintain consistent totals calculations. o Removed the fast.pe option for PE data handling, in favour of improved default processing. o Removed dumpPE(), which is not required without the fast.pe option. o Removed makeExtVector() in favour of list/DataFrame specification. o windowCounts() and regionCounts() now compute and store the mean PE size and read length. o Minor fix in correlateReads() for end-of-chromosome behaviour. o Modified checkBimodality() so that the width argument behaves like ext in windowCounts(). o extractReads() with as.reads=TRUE for PE data now returns a GRangesList. o Added the controlClusterFDR(), clusterWindows() and consolidateClusters() functions to automate control of the cluster-level FDR. o Added protection against NA values in the cluster IDs for combineTests(), getBestTest(), upweightSummits(). o All read extraction methods are now CIGAR-aware and will ignore soft-clipped parts of the alignment. Changes in version 1.4.0 o Added clusterFDR() function to compute the FDR for clusters of DB windows. o Added checkBimodality() function to compute bimodality scores for regions. o Modified normalize(), asDGEList() to allow manual specification of library sizes. o Switched from normalizeCounts(), normalize() to S4 method normOffsets(). o Modified default parameter specification in strandedCounts(), to avoid errors. o Switched to warning from error when a restricted chromosome is specified in extractReads(). o Modified extractReads() interface with improved support for extended read and paired read extraction. o Added normalization options to filterWindows() when using control samples. o Fixed bug for proportional filtering in filterWindows(). o Allowed correlateReads() to accept paired-end specification when extracting data. o Added maximizeCcf() function to estimate the average fragment length. o Added support for strand-specific overlapping in detailRanges(). o Increased the fidelity of retained information in dumped BAM file from dumpPE(). o Modified strand specification arguments for profileSites(), allowed reporting of individual profiles. o Removed param= specification from wwhm(). o Switched to RangedSummarizedExperiment conventions for all relevant functions. o Switched to mapqFilter for scanBam() when filtering on mapping quality. o Added tests for previously untested functions. o Slight updates to documentation, user's guide. Changes in version 1.2.0 o Added getWidths(), scaledAverage() and filterWindows(), to facilitate comparison of abundances during filtering. o Added findMaxima() to identify locally maximal windows from range data. o Added profileSites() to examine the coverage profile around specified regions, with wwhm() to guess the ideal window size from the profile. o Changed default window width in windowCounts() to 50 bp, default filter to a fixed count of 10. Also, filter=0 is honored when bin=TRUE. o Switched from the depracated rowData to rowRanges for all manipulations of SummarizedExperiment. o Changed all instances of `pet' to `pe' in read parameter specification, and renamed getPETSizes() to getPESizes(). o Removed the redundant rescue.pairs parameter in readParam(). o Added fast.pe parameter in readParam(), for fast paired-end data extraction. Added dumpPE() to pre-process paired-end BAM files for fast downstream extraction. o Added support for custom column specification in getBestTest(), combineTests(). o Switched from reporting average log-FC to numbers of up/down windows in combineTests(). o Allowed getBestTest() to return all fields associated with the best window in the output table. o Added upweightSummits() to compute weights favouring high-abundance windows. o Added combineOverlaps(), getBestOverlaps() and summitOverlaps() wrapper functions for processing of Hits objects. o Added consolidateSizes(), to consolidate DB results from multiple window sizes. o Added support for custom key/name specification in detailRanges() for non-human/mouse systems. o Added support for strand-specific read extraction in readParam(), strand-specific counting via strandedCounts(). o Added strand-awareness to mergeWindows(). Added protection against stranded input regions in extractReads(), detailRanges(). o Changed algorithm for splitting of large peaks in mergeWindows(). o Stored counting parameters in exptData for windowCounts(), regionCounts(). o Fixed small inaccuracies with continuity correction addition in normalizeCounts() for NB-loess. o Switched to fragment midpoint for binning of paired-end data in windowCounts(). o Added support for lists of library-specific readParam objects in windowCounts(), regionCounts(), correlateReads(). o Added makeExtVector(), to support variable read extension lengths between libraries in windowCounts(), regionCounts(). o Added support for read extension within extractReads(). o Updated the user's guide to reflect new and modified functions. o Added sra2bam.sh in inst/doc to reproducibly generate BAM files to run UG examples. o Cleaned up code in inst/tests for modified functions, added new tests for new functions. Changes in version 1.0.0 o New package csaw, for de novo detection of differential binding in ChIP-seq data.