Changes in version 1.18.0 o Added an intersect.genes= option to read10xCounts() for samples with inconsistent gene information. Automatically fix empty chromosome names for mitochondrial genes in certain Cellranger outputs. 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.