Changelog

Source: NEWS.md

BRGenomics 1.10.1 (release) & 1.11.1 (devel)

  • Updated the import_bam_ATAC() function with slightly revised options and operations
  • Fixed broken links in documentation

BRGenomics 1.0.3 (release) & 1.1.3 (devel)

  • 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

BRGenomics 1.0.1 (release) & 1.1.1 (devel)

  • 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

BRGenomics 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

BRGenomics 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

BRGenomics 0.99.25

BRGenomics 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)

BRGenomics 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)

BRGenomics 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

BRGenomics 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

BRGenomics 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

BRGenomics 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

BRGenomics 0.7.10

BRGenomics 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

BRGenomics 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

BRGenomics 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

BRGenomics 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()

BRGenomics 0.5.6

BRGenomics 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

BRGenomics 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

BRGenomics 0.4.7

BRGenomics 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

BRGenomics 0.4.1

  • Various documentation updates

BRGenomics 0.4.0

  • Added a NEWS.md file to track changes
  • Added support for bam files