NEWS
BRGenomics 1.11.1
- Updated the
import_bam_ATAC()
function with slightly revised options and
operations
- Fixed broken links in documentation
BRGenomics 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
BRGenomics 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
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
- 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
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
- Add
intersectByGene()
and reduceByGene()
functions
- Minor vignette updates
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
- 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()
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
- Rewrote
mergeGRangesData()
to support the creation of multiplexed GRanges
objects
- Made
getCountsByRegions()
and getCountsByPositions()
to return integers
if input signal is integer
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