Changes in version 1.31.1 - Update email address. Changes in version 1.29.1 - Fix the space inserted at the beginning after formatC for exportBamFile. Changes in version 1.27.4 - Fix the refresh issue for IGVSnapshot.R Changes in version 1.27.3 - Fix the issue if no single end reads in the PE bam files for shiftGAlignmentsList.R Changes in version 1.27.2 - Try to decrease the memory cost for shiftGAlignmentsList.R Changes in version 1.27.1 - Fix the issue caused by readGAlignmentsList does not support read by chunk Changes in version 1.25.2 - Add reNormalizeByDistalSig parameter to plotFootprints function. Changes in version 1.25.1 - Fix the error 'number of columns of matrices must match' for TSSEscore. Changes in version 1.23.1 - Add smooth function to TSSEscore. - Add pseudoPausingIndex function. Changes in version 1.21.2 - Add error message for NA seqlengths for factorFootprints.R Changes in version 1.21.1 - remove the limits of BSgenome object for vPlot Changes in version 1.19.3 - fix the email typo. Changes in version 1.19.2 - Change the method to fix the issue that NA is generated for conservation scores when call gscores. Changes in version 1.19.1 - Fix the issue that NA is generated for conservation scores when call gscores. Changes in version 1.17.1 - Fix the issue that NA is generated when no data available for TSSEscore. Changes in version 1.15.11 - Break the limitation of sequence length must have ends less than or equal to 536870912. Changes in version 1.15.10 - fix the issue that idxstatsBam return values with "*" Changes in version 1.15.9 - Add rmarkdown as suggest package. Changes in version 1.15.8 - update documentation for the case when no BSgenome object is available. Changes in version 1.15.7 - fix the NA values for TSSEscore when infinite value is in the data. Changes in version 1.15.6 - fix the missing link of documentation for rtracklyaer:import. Changes in version 1.15.5 - remove duplicates when shift reads. Changes in version 1.15.4 - Fix the issue when empty object input into exportBamFile. Changes in version 1.15.3 - Reuse header when exportBamFile in splitGAlignmentsByCut function. Changes in version 1.15.2 - Fix the tag MC in exportBamFile function. Changes in version 1.15.1 - write exportBamFile function to replace rtracklayer::export.bam. Changes in version 1.13.9 - fix the issue that plotCorrelation heatmap is scaled by row. Changes in version 1.13.8 - throw an error if not enought nucleosome free read nor mononucleosome reads for training. Changes in version 1.13.7 - fix a bug introduced by matchPWM by paste ^ and $ into exclude sequence name. Changes in version 1.13.6 - update documentation of plotFootprints. Changes in version 1.13.4 - fix a formular for TSSE score. Changes in version 1.13.3 - fix a bug the after shift, the index is not changed. Changes in version 1.13.2 - change the normalization method by library size for factorFootprints for user defined group samples. Changes in version 1.13.1 - Add documentation to decribe the format of bindingSites for factorFootprints. Changes in version 1.11.9 - Fix a issue for splitGAlignmentsList, splitGAlignments by supply the header info to mergeBam. Changes in version 1.11.8 - Fix a issue 'mergeBam' 'destination' exists, 'overwrite' is FALSE for splitGAlignmentsByCut. Changes in version 1.11.7 - fix a typo in doc for readBamFile. Changes in version 1.11.6 - fix the sample for shiftGAlignments. Changes in version 1.11.5 - add function shiftGAlignments for single end reads. Changes in version 1.11.4 - Fix the issue of if there is no reads in bam file for shiftGAlignmentsList. Changes in version 1.11.2 - Fix the issue of "[E::sam_parse1] unrecognized type N". Changes in version 1.11.1 - Add flag parameter for splitBam. Changes in version 1.9.9 - export prepareBindingSitesList function. - Add rownames for footprintsScanner counts data. Changes in version 1.9.8 - Add error message for vPlot when no paired reads in bam file. Changes in version 1.9.7 - Fix the bug that gscore changed the output for splitGAlignmentsByCut. Changes in version 1.9.6 - Try to decrease the memory cost for splitGAlignmentsByCut. Changes in version 1.9.5 - Try to decrease the memory cost for splitGAlignmentsByCut. Changes in version 1.9.4 - Add the error handle if not enough mononucleosome reads for splitGAlignmentsByCut. Changes in version 1.9.3 - Try to decrease the memory cost for splitGAlignmentsByCut. Changes in version 1.9.2 - Fix the bug if the bam file containsupplementary alignments. Changes in version 1.9.1 - Fix the bug if the bam file contain mix of single ends and paired ends. Changes in version 1.7.9 - add maximalBindingWidth parameter to footprintsScanner 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.