NEWS.md
In jianhong/ATACseqQC: ATAC-seq Quality Control
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.
jianhong/ATACseqQC documentation built on May 9, 2024, 2:21 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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
readGAlignmentsListdoes 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.copyinstead offile.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
classtois
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.