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