NEWS.md

In ATACseqQC: ATAC-seq Quality Control

CHANGES IN VERSION 1.14.4

• Fix the issue when empty object input into exportBamFile.

CHANGES IN VERSION 1.14.3

• Reuse header when exportBamFile in splitGAlignmentsByCut function.

CHANGES IN VERSION 1.14.2

• Fix the tag MC in exportBamFile function.

CHANGES IN VERSION 1.14.1

• 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.

ATACseqQC documentation built on Nov. 8, 2020, 11 p.m.