Changes in version 1.8.5 - Try to reduce the memory cost of splitGAlignmentsByCut. Changes in version 1.8.4 - Try to reduce the memory cost of splitGAlignmentsByCut. Changes in version 1.8.3 - Handle the error when there is not enough mononucleosome reads of splitGAlignmentsByCut. Changes in version 1.8.2 - Try to reduce the memory cost of splitGAlignmentsByCut. Changes in version 1.8.1 - Fix the bug if the bam file contail mix of single ends and paired ends. Changes in version 1.7.8 - change the function of footprintsScanner. Changes in version 1.7.7 - add parameter outPath for splitGAlignmentsByCut. Changes in version 1.7.6 - fix a bug in PTscore. Changes in version 1.7.5 - use file.copy instead of file.rename. Changes in version 1.7.4 - add parameter outbam for shiftGAlignmentsList. Changes in version 1.7.3 - Update documentation for Transcription start site (TSS) enrichment values Changes in version 1.7.2 - add the new biocViews tag "ImmunoOncology" Changes in version 1.7.1 - add more documentation for bigFile parameter in readBamFile.R Changes in version 1.5.7 - fix the memory issue of big bam file. Changes in version 1.5.6 - fix the bug when the reads length is smaller than 5 for shiftGAlignmentsList Changes in version 1.5.4 - export plotFootprints. Changes in version 1.5.3 - add Feng Yan as an author for function of estimateLibComplexity. Changes in version 1.5.2 - replace 'ds.mincount.bootstrap' with 'ds.rSAC.bootstrap' - add Transcription Start Site (TSS) Enrichment Score: TSSEscore Changes in version 1.5.1 - avoid NA in PTscores Changes in version 1.3.26 - Add index parameter for fragSizeDist and splitBam. Changes in version 1.3.25 - Add warning message for readsDupFreq when bam files without duplicates. Changes in version 1.3.24 - Fix a bug in NFRscore. Changes in version 1.3.23 - Move IGVSnapshot to extdata because it is not support windows. - add seqlenghts check for footprints. Changes in version 1.3.22 - Try to reduce the memory cost for bamQC. Changes in version 1.3.21 - Add doubleCheckDup parameter for bamQC. Changes in version 1.3.20 - fix the missing links in documentation. Changes in version 1.3.19 - fix the missing links in documentation. Changes in version 1.3.18 - Remove the dependence of SRAdb. Changes in version 1.3.17 - update vPlot. Changes in version 1.3.16 - copy getRelationship from ChIPpeakAnno. Changes in version 1.3.15 - add new function distanceDyad. Changes in version 1.3.14 - add new function vPlot. Changes in version 1.3.13 - fix a bug in footprintsScanner. - update the vignette. Changes in version 1.3.12 - improve the efficiency of bamQC. - add new function footprintsScanner. Changes in version 1.3.11 - update the documentation for function estimateLibComplexity, readsDupFreq, saturationPlot - fix a bug in saturationPlot.R ( using sum instead of cumsum for calculate the overall peak breadth) - improve the efficiency of bamQC. - add new function IGVSnapshot. Changes in version 1.3.10 - add new function plotCorrelation Changes in version 1.3.9 - add new functions readFreq, estimateLibComplexity and saturationPlot - output NRF, PBC1, and PBC2 from bamQC Changes in version 1.3.8 - add properPairRate, unmappedRate, hasUnmappedMateRate, notPassingQualityControlsRate in output of bamQC. Changes in version 1.3.7 - add mapq summary in output of bamQC. - add unit test for splitGAlignmentsByCut. Changes in version 1.3.6 - add unit test for factorFootprints and fragSizeDist. Changes in version 1.3.5 - adjust the Cut-site probability by the depth=librarySize/libraryCoverageSize for output of factorFootprints Changes in version 1.3.4 - Add function PTscore and NFRscore - add Profile.segmentation in output of factorFootprints - add unit test. Changes in version 1.3.3 - Fix a bug in factorFootprints when bindingSites is supplied. - Modified the vignettes. - Expand the functionality of the bamQC function. - Import motifStack. Changes in version 1.3.2 - Fix a bug in factorFootprints when bindingsite is less than 2. Changes in version 1.3.1 - Fix a bug in factorFootprints Changes in version 1.1.17 - add gal argument for enrichedFragments to improve the efficency. Changes in version 1.1.16 - Fix a bug in fragSizeDist Changes in version 1.1.15 - Fix a bug in bamQC Changes in version 1.1.14 - Fix the error: when 'type' is "any", at least one of 'maxgap' and 'minoverlap' must be set to its default value Changes in version 1.1.13 - improve the efficency of factorFootprints. Changes in version 1.1.12 - fix the soft clipping and improve the efficency. Changes in version 1.1.11 - fix a bug in fragSizeDist. Changes in version 1.1.10 - Check is PE before run fragSizeDist. Changes in version 1.1.9 - Remove duplicates for outputs of bamQC. Changes in version 1.1.8 - Add function bamQC. Changes in version 1.1.7 - Fix a bug in shiftGAlignmentsList. Changes in version 1.1.6 - Change default behavior of splitBam Changes in version 1.1.5 - update the vignette. Changes in version 1.1.4 - change author list. Changes in version 1.1.3 - change output of factorFootprints. Changes in version 1.1.2 - add cumulativePercentage in vignette Changes in version 1.1.1 - add new author. Changes in version 0.99.8 - reduce the memory cost. Changes in version 0.99.7 - update phastCons to GScores. Changes in version 0.99.6 - update documentation - change package Name from ATACqc to ATACseqQC - remove unused dependence - change class checking from class to is Changes in version 0.99.5 - add bindingSites argument for factorFootprints Changes in version 0.99.4 - change shiftBam to shiftGAlignmentsList - drop seqlevs arguments from functions Changes in version 0.99.3 - try to avoid error in windows that splitBam ask too much memory Changes in version 0.99.2 - change function name from splitBamByCut to splitGAlignmentsByCut - add function shiftBam and writeGAlignmentsList - rewrite splitBam function by just call shiftBam, splitGAlignmentsByCut and writeGAlignmentsList. Changes in version 0.99.1 - fix the bug "object inverted is not exported by 'namespace:Biostrings'" Changes in version 0.99.0 - Submit to Bioconductor. Changes in version 0.1.0 - Create the package.