- fix example errors
 

 updating NBTest function
 

 added test for fix of Issue #6
 

 update migration_notes.md
 

 Update version and news
 

 updates
 

 adding references and versions.
 

 Update for Rhtslib compatibility. (Patch by Hervé Pagès)
 

 Added error message if gene id is not present in expression set (for main prediction algorithm and scoring)
 

 appveyor.yml v10
 

 appveyor.yml v9
 

 fixed rbamtools dependency
 

 Removing obsolete Windows config file
 

 Updated configure file for hidden source file
 

 Removed uncalled macro from configure.ac and updated cleanup script
 

 Modify Makevars.in to substitute kludge for 'abort'
 

 Kludge to eliminate warning from boost call to 'abort'
 

 Link to headers in installed package CRAN BH
 

 Added a missing return

 

 add numerical filtering
 

 add detailed infos after aggregation
 

 version
 

 updates

Merge branch 'master' of git.bioconductor.org:packages/MACPET

# Conflicts:
#	DESCRIPTION
 

 date
 

 version update as well as packages update
 

 version 1.15.12 : add numerical filtering
 

 Removed a logical comparison longer than 1

 

 Fix bug in buildPed, prune = TRUE resulting in missing parents

- Fix a bug in buildPed with prune = TRUE that resulted in either a missing
  mother or father for some complicated pedigrees.
 

 remove import genome
 

 version bump
 

 devel version bump
 

 Add README.md
 

 Enable LFS.
 

 Progress bar edit and unecessary code removal
 

 deprecate some api
 

 run roxygen
 

 rm flowjo parsing code
 

 fix test-copyNode
 

 eliminate the path generation for allNodes #280
 

 set path='full' by default for getPopStats #280
 

 Update travis.yml
 

 Make parseWorkspace guid format and warnings match cytoset branch
 

 bump
 

 update vignette
 

 rm dep on xml
 

 include Rcpp header after cytolib to avoid masking pb macro defs by R
 

 Update .travis.yml 

 parallel getPopStats #280
 

 switch from vector to deque for efficient gate path handling. #280
 

 speed up get_leaf_node
 

 bump
 

 bump
 

 Merge branch 'trunk' of github.com:RGLab/flowWorkspace into trunk
 

 Rename use.sampleID to additional.sampleID and add doc
 

 Improve copyNode recursion
 

 roxygenize getFullNodePath
 

 bump
 

 Make parseWorkspace throw error for duplicated FCS in workspace
 

 Merge branch 'trunk' of github.com:RGLab/flowWorkspace into trunk
 

 overload identifier method and avoid direct access to guid slot
 

 merge conflicts
 

 Add guid slot to GatingSetList
 

 Add methods for transforming gates from nodes in GatingHierachy/GatingSet
 

 rerun roxgyen
 

 bump
 

 add flowJo parser from flowWorkspace
 

 merge trunk
 

 Add ImmunoOncology biocViews term
 

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 

 rename getPopPaths to getNodePaths and move the logic into and call getNodePath API
 

 call queryByPath instead of getNodeId to avoid exception overhead for getPopPaths. RGLab/flowWorkspace#280
 

 v1.13.5 release
 

 update docs, and vectorized code #266 #267
 

 add axis lims and segment size options
 

 Address #255
 

 address #256
 

 Address #254
 

 update news
 

 Merge pull request #251 from JohnMCMa/master

Implement showMutationRate argument in lollipopPlot 

 update news
 

 address variable name coflicts
 

 address #241 #244
 

 Address #241 and #242
 

 base graphics
 

 Change default value for mafObj to TRUE
 

 address #214
 

 Added lots of performance improvements, also fixed rezvans improvement (disjunctive common ancestors were not being calculated).
 

 Add modulePlots
 

 Forgot to add .gitignore in last commit
 

 fix dox
 

 bug fix in daFrame-constructor
 

 Fixed a typo in error message
 

 hide Rsubread messages if verbose == FALSE in alignRsubread
 

 fixed test using && instead of &
 

 appveyor.yml v6
 

 appveyor.yml now install TFBSTools v5
 

 appveyor.yml now install TFBSTools v3
 

 appveyor.yml now install TFBSTools
 

 cpp code changes, .travis.yml changes
 

 export replaceCOLS()
 

 Merge branch 'RELEASE_3_8'

version 1.5.6: (2019-03-20) - merge from RELEASE_3_8 branch
- Bug fix when not providing BatchInfo as factor
- Extra check if batch names contain spaces
- Added line breaks after individual error messages
- Bug fix that corrects for the number of factors in BatchInfo vector
- Small bug fix in 'test_mcmc_arguments.R'
 

 version 1.4.5: (2019-03-20)
- Small bug fix in 'test_mcmc_arguments.R'
 

 Minor commit
 

 version 1.4.3 (2019-03-15)
 

 Add ImmunoOncology biocViews term
 

 bug fix: use BiocGenerics::relist
 

 re-use helper functions, expand functionality
 

 splitAssays clean up and add exclusive argument
 

 Fix non-ASCII character
 

 version bump to prod bioc to see new CITATION file
 

 version bump
 

 One test modified
 

 Code refactoring
 

 Almost finished touching up, running checks and fixing tests...
 

 Added Rezvans new improvement and reformatted slightly
 

 Fixed bug in kpAddCytobandsAsLine with plot.type!=1

 

 documentes a coupld of points

 

 Merge branch 'RevampGenes' 

 Added improved gene name selection

 

 Added mergeTranscripts function

 

 Created a package wide structure to hold color schemas and color info

Created a package wide structure to hold color schemas and color info and adapted getCytobandColors and getVariantsColors. Adapted the two functions to use the colors from the package-wide structure 

 Added addGeneNames to add the symbols to the GenesData object

 

 Added metadata to GenesData object when created from TxDb

 

 Added a couple of TODOs

 

 Added a section to README.md with examples

 

 Changed cut.last.tile.in.chrom to TRUE in kpPlotDensity

To ensure all windows (except the last in the chromosome) have the same length. In response to https://github.com/bernatgel/karyoploteR/issues/30 

 Added colByRegion function

 

 changes in readme
 

 python code
 

 add trimColData function, update examples, include pkgs in Suggests
 

 bug fix: c method when named list provided
 

 remove _pkgdown.yml from devel ver.
 

 Preparing multiple GISTIC files #304
 

 Fix buildPed and pedigree<-

- Fix bugs in buildPed and pedigree<- for some special cases.
 

 Merge branch 'master' into haplopainter_bug
 

 Re-introduce "-family" parameter for haplopainter.

This option has been removed during a refactoring process (issue #16).
However, it's a mandatory parameter in the haplopainter command line, causing
an error message when calling the haplopainter Perl script.
 

 pseudocount added after compositionality in CLR

when making a CLR tranformation, transform to compositional before
adding the small v/2 pseudocount to ensure that the prior induced by the
pseudocount is constant across varying library sizes.
 

 ok
 

 sync
 

 ok
 

 Update README.md 

 Update README.md 

 v1.23.17 qQCReport updates
 

 Fix usage section qQCReport
 

 Fix qQCReport docs
 

 Merge pull request #11 from hrhotz/patch-1

Update qQCReport.Rd 

 re-enable appveyor cache 

 delete appveyor cache 

 Fix subplot sizes for mapping/uniqueness plots to work with a single sample
 

 Update qQCReport.Rd

This is a quick fix following the question on the BioC mailing list (https://support.bioconductor.org/p/118580/). It is still not correct, e.g. what happens when you generate a qProject with bam files which do not contain the quality.....

Hence, it is rather work in progress and should not be merged yet, but might trigger a discussion. 

 Allow the df of expression.values to have fewer rows than the transcript file.
 

 fix documentation link to S4Vectors::DataFrame
 

 - Update simReads.Rd to match code.
- Make simFragments and fix_simReads non-exported functions.
 

 - library.size instead of out.sample.size.
- make defaults for fragment size distn in simReads agree with simFragments.
 

 Fix spelling of "Occurrence"
 

 updated news, version bump for changes
 

 Correct version for sync with bioconductor
 

 Merge pull request #13 from DavisLaboratory/issue_7

Issue 7 

 singscore now supports scoring of multiple signatures. Code restructured to achieve this and reduce code redundancy. Changed signature of simple score from ANY to matrix for rankData param.
 

 fixed issue with checking annotations that was throwing warnings for character annotations
 

 updated the NEWS file
 

 plot title size increased
 

 remove old code
 

 new structure for scoring functions implemented. Modular structure will ease integration of scoring function that scores multiple signatures
 

 Merge branch 'master' of github.com:DavisLaboratory/singscore

Changed colours of the plotRankDensity to be colour-blind friendly
 

 Merge pull request #12 from DavisLaboratory/issue_9

automatically select the number of bins as sqrt(num_obs) 

 Merge pull request #11 from DavisLaboratory/issue_10

Issue 10 

 updated citation and re-built site
 

 numeric, factor and column of data.frames can now be used as annotations for static plots. Plot style updated. Need to extend functionality to interactive plots.
 

 plotDispersion can now deal with different forms of annotations incl. factors, numerics and columns appended to the score data.frame
 

 update website
 

 modify NEWS.md to comply with website format
 

 added a git ignore
 

 fix unit test filename
 

 loading helper function tests
 

 don't coerce to dense matrix when calcing pofgenes
 

 tidied rankmetrics options
 

 Added new rankmetrics for evalation, and n parameter.
 

 Add dgamma and rmultinom to NAMESPACE imports
 

 Fix a bug
 

 Anonynous input matrix
 

 fixing bug in computing the score in broadPeaks function with HDF5 backend
 

 Minor changes
 

 version bump
 

 Improve bug fix in commit 167fcdfcf3077be16db54cd6ce8590a77ca391e8

- Document why fix is necessary with new mapToTranscripts() behavior
- Implement fix for predictCoding(). The last commit only addressed
  locateVarants().
 

 removed rbamtools dependency
 

 reducing dependencies and imports
 

 Rethink check for Authors@R vs Author/Maintainer

  - the check worked fine on open directories
  - when R does R CMD build, and then that tar is untarred, the additional Author and Maintainer fields where added based on Author@R so the check is always positive resulting in false positives
 

 cleaned up memory setting; should be every so slightly faster
 

 Merge branch 'master' of github.com:vsbuffalo/qrqc
 

 fixed bug with ggplot and basePlot
 

 fixed typo in show methods
 

 fixed doc issues
 

 minor changes to avoid linux build warnings
 

 few documention changes
 

 added k-mer doc
 

 added doc on new KL methods
 

 changes made to kmer handing, info theo approaches
 

 fixed bug with k-mer handling (stopping before end)
 

 added positional k-mer hashing, plots, accessors
 

 removed phred quality, added blurb about qualities in readseqfile
 

 new vignette
 

 fixed some build issues with doc
 

 additions to readme, added more ggplot2 fun doc
 

 added doc templates, some new doc
 

 readme/description changes, minor plot additions
 

 added geom bar for basePlot
 

 added new ggplot-based plotting functions
 

 fixed issue in io.c with phred quality, added GNU-style change log
 

 small bug fixes - removed called to browser(), error in Sanger/Phred quality schemes
 

 version bump
 

 version bump
 

 fixed issue
 

 fixed Makefile, doc aliases, and Makevars
 

 removed RColorBrewer Dependency
 

 version bump
 

 fixed report output directory, added legend
 

 added Makevars for windows
 

 version bump for last change
 

 version bump for last change to gzreadclone
 

 version bump, fixed s4 method documentation, added NEWS
 

 to resolve windows portability (no zlib.h), KSEQ_INIT is given clone function when _WIN32 defined
 

 minor change to gitignore to ignore tex auto directories
 

 added vignette draft
 

 new methods for FASTA and FASTQ files
 

 moved more functions to utils.R, added more test functions
 

 moved methods and generics to own files to follow Bioconductor package guidelines, wrote generic wrappers around all plotting functions, fixed offset-by-1 issue with plotQuals
 

 added man page for SequenceSummary class
 

 added man page for readSeqFile
 

 fixed bug with plotSeqLengths
 

 added basic unit testing of some functions
 

 initial show method outlined
 

 Initial outline of S4 system, plus moving graphics functions to graphics.R

- New items in TODO
- Renamed scan.R to main.R
 

 version bump; namespace added, and description edited
 

 finished plot with histogram and proper labels
 

 refactored, fixed seq.length issue
 

 working refactor around kseq.h sequence reading library
 

 minor grammar change to DESCRIPTION
 

 added more function documentation
 

 added sequence length statistics
 

 cleaner mean plotting character
 

 improved empirical quantile handling
 

 added test data file
 

 changed protect to PROTECT, removed unused function
 

 fixing misnamed variable, again
 

 basic quantile function from binned data, and qual linerange plots
 

 fixed issue with lack of strdup, which lead to improper sequence names
 

 changed output verbosity level to be based on nblocks
 

 unique count was incorrect - fixed
 

 try higher initial hash size