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.