- Update email address.
- Fix the space inserted at the beginning after formatC for exportBamFile.
- Fix the refresh issue for IGVSnapshot.R
- Fix the issue if no single end reads in the PE bam files for shiftGAlignmentsList.R
- Try to decrease the memory cost for shiftGAlignmentsList.R
- Fix the issue caused by
readGAlignmentsListdoes not support read by chunk
- Add reNormalizeByDistalSig parameter to plotFootprints function.
- Fix the error 'number of columns of matrices must match' for TSSEscore.
- Add smooth function to TSSEscore.
- Add pseudoPausingIndex function.
- Add error message for NA seqlengths for factorFootprints.R
- remove the limits of BSgenome object for vPlot
- fix the email typo.
- Change the method to fix the issue that NA is generated for conservation scores when call gscores.
- Fix the issue that NA is generated for conservation scores when call gscores.
- Fix the issue that NA is generated when no data available for TSSEscore.
- Break the limitation of sequence length must have ends less than or equal to 536870912.
- fix the issue that idxstatsBam return values with "*"
- Add rmarkdown as suggest package.
- update documentation for the case when no BSgenome object is available.
- fix the NA values for TSSEscore when infinite value is in the data.
- fix the missing link of documentation for rtracklyaer:import.
- remove duplicates when shift reads.
- Fix the issue when empty object input into exportBamFile.
- Reuse header when exportBamFile in splitGAlignmentsByCut function.
- Fix the tag MC in exportBamFile function.
- write exportBamFile function to replace rtracklayer::export.bam.
- fix the issue that plotCorrelation heatmap is scaled by row.
- throw an error if not enought nucleosome free read nor mononucleosome reads for training.
- fix a bug introduced by matchPWM by paste ^ and $ into exclude sequence name.
- update documentation of plotFootprints.
- fix a formular for TSSE score.
- fix a bug the after shift, the index is not changed.
- change the normalization method by library size for factorFootprints for user defined group samples.
- Add documentation to decribe the format of bindingSites for factorFootprints.
- Fix a issue for splitGAlignmentsList, splitGAlignments by supply the header info to mergeBam.
- Fix a issue 'mergeBam' 'destination' exists, 'overwrite' is FALSE for splitGAlignmentsByCut.
- fix a typo in doc for readBamFile.
- fix the sample for shiftGAlignments.
- add function shiftGAlignments for single end reads.
- Fix the issue of if there is no reads in bam file for shiftGAlignmentsList.
- Fix the issue of "[E::sam_parse1] unrecognized type N".
- Add flag parameter for splitBam.
- export prepareBindingSitesList function.
- Add rownames for footprintsScanner counts data.
- Add error message for vPlot when no paired reads in bam file.
- Fix the bug that gscore changed the output for splitGAlignmentsByCut.
- Try to decrease the memory cost for splitGAlignmentsByCut.
- Try to decrease the memory cost for splitGAlignmentsByCut.
- Add the error handle if not enough mononucleosome reads for splitGAlignmentsByCut.
- Try to decrease the memory cost for splitGAlignmentsByCut.
- Fix the bug if the bam file containsupplementary alignments.
- Fix the bug if the bam file contain mix of single ends and paired ends.
- add maximalBindingWidth parameter to footprintsScanner
- change the function of footprintsScanner.
- add parameter outPath for splitGAlignmentsByCut.
- fix a bug in PTscore.
- use
file.copyinstead offile.rename.
- add parameter outbam for shiftGAlignmentsList.
- Update documentation for Transcription start site (TSS) enrichment values
- add the new biocViews tag "ImmunoOncology"
- add more documentation for bigFile parameter in readBamFile.R
- fix the memory issue of big bam file.
- fix the bug when the reads length is smaller than 5 for shiftGAlignmentsList
- export plotFootprints.
- add Feng Yan as an author for function of estimateLibComplexity.
- replace 'ds.mincount.bootstrap' with 'ds.rSAC.bootstrap'
- add Transcription Start Site (TSS) Enrichment Score: TSSEscore
- avoid NA in PTscores
- Add index parameter for fragSizeDist and splitBam.
- Add warning message for readsDupFreq when bam files without duplicates.
- Fix a bug in NFRscore.
- Move IGVSnapshot to extdata because it is not support windows.
- add seqlenghts check for footprints.
- Try to reduce the memory cost for bamQC.
- Add doubleCheckDup parameter for bamQC.
- fix the missing links in documentation.
- fix the missing links in documentation.
- Remove the dependence of SRAdb.
- update vPlot.
- copy getRelationship from ChIPpeakAnno.
- add new function distanceDyad.
- add new function vPlot.
- fix a bug in footprintsScanner.
- update the vignette.
- improve the efficiency of bamQC.
- add new function footprintsScanner.
- 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.
- add new function plotCorrelation
- add new functions readFreq, estimateLibComplexity and saturationPlot
- output NRF, PBC1, and PBC2 from bamQC
- add properPairRate, unmappedRate, hasUnmappedMateRate, notPassingQualityControlsRate in output of bamQC.
- add mapq summary in output of bamQC.
- add unit test for splitGAlignmentsByCut.
- add unit test for factorFootprints and fragSizeDist.
- adjust the Cut-site probability by the depth=librarySize/libraryCoverageSize for output of factorFootprints
- Add function PTscore and NFRscore
- add Profile.segmentation in output of factorFootprints
- add unit test.
- Fix a bug in factorFootprints when bindingSites is supplied.
- Modified the vignettes.
- Expand the functionality of the bamQC function.
- Import motifStack.
- Fix a bug in factorFootprints when bindingsite is less than 2.
- Fix a bug in factorFootprints
- add gal argument for enrichedFragments to improve the efficency.
- Fix a bug in fragSizeDist
- Fix a bug in bamQC
- Fix the error: when 'type' is "any", at least one of 'maxgap' and 'minoverlap' must be set to its default value
- improve the efficency of factorFootprints.
- fix the soft clipping and improve the efficency.
- fix a bug in fragSizeDist.
- Check is PE before run fragSizeDist.
- Remove duplicates for outputs of bamQC.
- Add function bamQC.
- Fix a bug in shiftGAlignmentsList.
- Change default behavior of splitBam
- update the vignette.
- change author list.
- change output of factorFootprints.
- add cumulativePercentage in vignette
- add new author.
- reduce the memory cost.
- update phastCons to GScores.
- update documentation
- change package Name from ATACqc to ATACseqQC
- remove unused dependence
- change class checking from
classtois
- add bindingSites argument for factorFootprints
- change shiftBam to shiftGAlignmentsList
- drop seqlevs arguments from functions
- try to avoid error in windows that splitBam ask too much memory
- change function name from splitBamByCut to splitGAlignmentsByCut
- add function shiftBam and writeGAlignmentsList
- rewrite splitBam function by just call shiftBam, splitGAlignmentsByCut and writeGAlignmentsList.
- fix the bug "object inverted is not exported by 'namespace:Biostrings'"
- Submit to Bioconductor.
- Create the package.