Changes in version 1.11.1
- Updated the import_bam_ATAC() function with slightly revised options
and operations
- Fixed broken links in documentation
Changes in version 1.1.3
- Increased safeguards against automatic vector coercion of matrices
and dataframes
- Increased tolerance of the precision workaround in
getStrandedCoverage() (workaround releveant to GenomicRanges issue
#39; will be obviated in next major Bioconductor release)
- Various minor efficiency & formatting changes
Changes in version 1.1.1
- Merge changes from 0.99.33 into release branch
- Bug workaround for getStrandedCoverage() and dependent methods for
getting coverage of normalized data (apparent bug in
IRanges::coverage() for weighting by normalized values)
- Bug fix in getCountsByPositions() for getting counts over an
unstranded region with expand_ranges=TRUE
Changes in version 0.99.33
- Add support for log fold-change shrinkage in getDESeqResults()
- Minor bugfix generating a warning under some conditions when
non-integer binsizes are used
Changes in version 0.99.30
- Change all ncores options to default to getOption("mc.cores", 2L)
- Rename n-dimensional binning functions aggregateByNdimBins() and
densityInNdimBins()
- Redone documentation website, splitting up the vignette
- Updated package vignettes/guide pages in several places
- Other minor internal changes
Changes in version 0.99.25
- Bug fixes with expand_ranges arguments affecting
getCountsByRegions(), subsampleGRanges(), and getSpikeInNFs()
- Expanded testing, particularly for expand_ranges arguments and
import_bam()
- Added options in mergeReplicates()
- Various small doc updates and minor internal changes
Changes in version 0.99.23
- Added support for non-basepair-resolution GRanges throughout, via
the expand_ranges argument
- Substantial performance benefits for less-sparse datasets (e.g.
whole read coverage)
- Supported everywhere, including counting functions, subsampling,
merging, normalization, etc.
- Rewrite of mergeGRangesData():
- Substantial performance improvements for most datasets
- No longer requires basepair-resolution GRanges objects
- Added options and flexibility for merging reads as well as
coverage data
- Add a mergeReplicates() function
- Rewrite of makeGRangesBRG() that significantly improves performance
for sparser datasets (the datasets for which using the function
makes the most sense)
- subsampleGRanges() no longer returns a basepair-resolution GRanges
by default
- When field=NULL, applyNFsGRanges() no longer returns a
basepair-resolution GRanges by default
- Add use_bin_numbers option to n-dimension binning functions; setting
to false allows returning of bin values (the bin center) instead of
the ordinal bin numbers (indexes)
- Quietly adding support for GRangesList objects (not fully tested)
Changes in version 0.99.15
- Add pre-filtering to counting functions for performance
- Some additional clarification of readcounts vs. coverage signal in
counting and import functions
- Change tidyChromosomes test
- Remove indirect links in doc pages (use only exact names of man
pages)
Changes in version 0.99.10
- Code modifications to pass Bioconductor test builds on Windows:
- Make all examples and tests single core
- Internally (not exported) redefine mcMap (current implementation
in package parallel needs to be modified)
- In tests and examples, test if on Windows before attempting any
bigWig file import
Changes in version 0.99.0
- Changes for Bioconductor submission:
- Move to package versioning 0.99.x
- Update R requirement to version 4.0
- Add new branch R3 to allow users to install under R version
>=3.5
- Various minor formatting changes to codebase
Changes in version 0.8.1
- Fixed bug in import_bam() that produced warnings when shift argument
used to shift both 5' and 3' ends of reads (i.e. when length(shift)
== 2)
- Updated included external datasets to be much smaller
- Included bam file now <200 reads
- Included bigWig and bedGraph files derived from the bam file
- Minor update to vignette to reflect the change in the bam file
- Updated the included data() objects (PROseq and PROseq_paired)
- Shifted PRO-seq 3' bases to remove the run-on base, and updated
associated package tests
- Added xz compression to the files
- Streamlined some method dispatch in genebodies() and
getDESeqDataSet() functions
Changes in version 0.8.0
- Add support for lists in data import functions
- Add the convenience function applyNFsGRanges()
- Significant internal changes to import_bam()
- New test for paired-end reads (deprecated use of
Rsamtools::testPairedEndBam())
- Avoids any internal use of bpiterate()
- Dropped dependency on GenomicFiles package
Changes in version 0.7.10
- Add intersectByGene() and reduceByGene() functions
- Minor vignette updates
Changes in version 0.7.8
- Substantially updated vignette
- Fully load rtracklayer (so completely exported to users)
- Add isBRG() function
- Fixed bug in spikeInNormGRanges() that failed to remove spike-in
reads (aside from maintaining those reads, normalization was
otherwise correct)
- Fixed minor bug in which metaSubsample() automatically added
rownames with list input
Changes in version 0.7.7
- Bug fix in aggregateByNdimensionalBins() affecting simultaneous
aggregation of multiple data
- Minor updates to documentation, including an error in
getDESeqResults()
- Slightly expanded vignette
Changes in version 0.7.5
- Update bootstrapping functions
- Add blacklisting support for metaSubsample()
- Related to blacklisting, NA values now ignored in bootstrapping
- Add additional melt options for signal counting functions
- Further expanded support for list inputs (lists of GRanges
datasets), including in getStrandedCoverage()
- Add explicit support for blacklisting in getDESeqDataSet()
- Rewrite n-dimensional binning functions, and add function for
aggregating data within n-dimensional bins
- Changed arguments in binNdimensions() to only accept dataframe
inputs
- Add densityInNdimensionalBins() function to count points in each
bin
- Add aggregateByNdimensionalBins() function to aggregate data
within bins using arbitrary functions
- Added arguments for setting sample names in spike-in/normalization
functions
- Various improvements and streamlining for method dispatch and
flexibility
Changes in version 0.7.0
- Added functions for counting and filtering spike-in reads
- Added functions for generating spike-in normalization factors
- Added support for lists of GRanges datasets throughout, including
all signal counting functions
- Updating signal counting functions with a blacklist argument, for
ignoring reads from user-supplied regions
- Added wrappers for import_bam() for several common use cases
- Update getCountsByPositions():
- Added a melt option for returning melted dataframes
- Now returns an error by default if multi-width regions are given
(must be explicit)
- Changed argument order in getMaxPositionsBySignal()
Changes in version 0.5.6
- Update import_bam() function
- Added support for paired-end bam files
- Added the shift argument
- Made metaSubsample() functions robust to unevaluated inputs
- Small performance improvement to genebodies() function
- Multicore usage is again the default for getDESeqResults()
Changes in version 0.5.3
- Substantial performance improvement for mergeGRangesData()
- Make single-core the default for getDESeqResults()
- Fixed errant warning message in binNdimensions() for integer inputs
- Update namespace to fully import GenomicRanges and S4Vectors
- Changed R dependency, evidently required by the updated data objects
- Various documentation updates
- Added package documentation page
- Minor changes to examples
Changes in version 0.5.0
- Increased support for multiplexed GRanges objects across all
functions
- Increased performance for bootstrapping over multiple
fields/multiplexed GRanges objects
- Removed requirement to set 'field' argument for gettings counts over
multiplexed GRanges
Changes in version 0.4.7
- Rewrote mergeGRangesData() to support the creation of multiplexed
GRanges objects
- Made getCountsByRegions() and getCountsByPositions() to return
integers if input signal is integer
Changes in version 0.4.5
- Added and modified numerous arguments
- Increased support for normalization factors across signal counting
functions
- Modified behavior of bootstrapping over multiple fields by removing
explicit access to .Random.seed
Changes in version 0.4.1
- Various documentation updates
Changes in version 0.4.0
- Added a NEWS.md file to track changes
- Added support for bam files