Changes in version 1.12.0
o Added BPPARAM= to read10xCounts() for parallelized reading of
multiple samples.
o Gave all the *Ambience() functions better names, and
soft-deprecated the current versions.
o Added ambientContribSparse() to estimate the ambient
contribution under sparsity assumptions.
o Added cleanTagCounts() to remove undesirable barcodes from tag
count matrices.
o Converted all matrix-accepting functions to S4 generics to
support SummarizedExperiment inputs.
o emptyDrops() will now coerce all DelayedArray inputs into
wrapped SparseArraySeeds.
o Setting test.ambient=TRUE in emptyDrops() will no longer alter
the FDRs compared to test.ambient=FALSE. Added test.ambient=NA
to retain back-compatible behavior.
o Bugfix for correct use of redefined lower when by.rank= is set
in emptyDrops().
o Added a constant.ambient=TRUE option to hashedDrops() to better
support experiments with very few HTOs.
Changes in version 1.10.0
o Migrated downsampleMatrix() to scuttle with a re-export.
o Added features= to downsampleReads() for per-feature-set
downsampling.
o Added matrix support for y= and ambient= in maximumAmbience().
o Added controlAmbience() for easy estimation of ambient
contamination with control features.
o Added removeAmbience() function to remove the ambient solution
from a count matrix, mostly for aesthetics.
o Report library index and feature type in output of
read10xMolInfo().
o Support subsetting by library index/type in functions that use
the molecule information file, such as swappedDrops() and
chimericDrops().
o Added by.rank= option to estimateAmbience() and emptyDrops(),
for estimation of the ambient profile by excluding barcodes
with the largest totals.
o Added exclude.from= option to barcodeRanks(), to avoid problems
with instability at low ranks for knee/inflection calculations
(contributed by Stefano Mangiola).
o Minor bugfix in barcodeRanks() calculation of the knee point.
Note that this affects the default choice of retain= in
emptyDrops().
o Split off HTO ambience inferences into a separate
inferAmbience() function.
o Added support for combinatorial barcodes in hashedDrops().
Changes in version 1.8.0
o Added the downsampleBatches() function for convenient
downsampling of batches.
o Preliminary support for using the output of write10xCounts()
back in Cellranger.
o Support reading in 10X output files via prefixes in
read10xCounts(). Automatic detection of whether a file is
Gzipped or not.
o Added chimericDrops() to remove chimeric molecules due to
within-sample re-priming.
o Added hashedDrops() to demultiplex cell hashing experiments.
o Added maximumAmbience() to estimate the maximum contribution of
the ambient profile.
Changes in version 1.6.0
o Switched emptyDrops() to use Boost's discrete_distribution for
weighted sampling. This results in some minor stochastic
changes to the Monte Carlo p-values. Automatically round
non-integer count matrices.
Changes in version 1.4.0
o Removed read10xMatrix().
o Supported CellRanger v3 output files in read10xMolInfo(),
read10xCounts(), write10xCounts().
o Modified barcodeRanks() to return a DataFrame with
knee/inflection estimates in metadata.
o Slight change to random number generation in emptyDrops() to be
agnostic to number of cores.
Changes in version 1.2.0
o Added removeSwappedDrops() for removing swapping in other types
of droplet-based data.
o Added alpha= argument to testEmptyDrops() to support
overdispersion during sampling. Returned arguments and
estimates in metadata of testEmptyDrops(), emptyDrops().
o Added encodeSequences() for convenient 2-bit encoding of
sequences.
o Added get10xMolInfoStats() function to compute per-cell
statistics from a molecule info file.
o Deprecated read10xMatrix(), as it does not add much practical
value over Matrix::readMM().
o Support the 10X sparse HDF5 format in read10xCounts().
o Support the 10X sparse HDF5 format in write10xCounts().
Changes in version 1.0.0
o
New package DropletUtils, for handling droplet-based
single-cell RNA sequencing data.