Removed the 'maxMOp' parameter from featureCounts.
Add support for ARM64 platforms.
Add support for CBCL format in cellCounts.
Improve the data structure used by cellCounts to further improve its speed.
More checks for input parameters to prevent cellCounts from crashing.
Improve the screen output of cellCounts.
Added inbuilt RefSeq annotation for mm39 (mouse genome Build 39).
Streamlined the mapping and counting processes in cellCounts.
Added support for processing dual-index 10x data in cellCounts.
Improved the speed of cellCounts and also reduced its memory use.
Added a parameter 'umi.cutoff' to cellCounts to call all the cells that had a total UMI count greater than the specified threshold.
Added support for FASTQ-format read input in CellCounts.
The 'isPairedEnd' parameter in featureCounts() is now used to check if the type of input reads (paired-end or single-end) is correctly specified.
A new parameter 'countReadPairs' was added to featureCounts to specify if read pairs should be counted for paired-end read data.
Changes to the input parameters and output of cellCounts() function. CellCounts will generate a Sample Sheet for samples included in the scRNA-seq data, based on the sample index set name provided by the user. Structure of the List object returned by cellCounts() is also simplified. cellCounts() now also outputs a BAM file and a gzipped FASTQ file including raw reads for each sample.
Improve cellCounts() on the identification of cell barcodes arising from ambient RNAs.
Rsubread package is ported to Windows OS.
New function cellCounts(): generate UMI counts for Chromium 10X single-cell RNA-seq data.
flattenGTF() function can merge or chop overlap features.
Check and display the amount of memory available on the computer before starting read mapping.
Optimize the data structure used in buildindex() function to reduce its memory use.
qualityScores() function can optionally retrieve quality scores from all the reads.
File paths included in column names of objects returned by featureCounts(), align(), subjunc() and propmapped() functions are removed or shortened where appropriate.
featureCounts() will be terminated if both single-end and paired-end reads are found in the same input file.
Limit on the length of input file names is increased to 1000 bytes for all functions.
New functions: simReads() and scanFasta(). simReads() generates simulation RNA-seq reads for transcripts.
align() and subjunc() estimate fragment length from mapped read pairs and use the estimated length to assist reporting the best alignment.
align() and subjunc() prefer alignments with no indels included over indel-containing alignments when same number of matched bases are found.
align() and subjunc() check if index files were successfully loaded before starting read mapping.
align() and subjunc() detect indels arising from incorrect shifting of seed sequence when being mapped to low-complexity region and exclude such indels from read re-alignment and indel reporting.
buildindex(), align() and subjunc() support gzipped FASTA format.
featureCounts() allows mapped reads to have ‘*’ as their chromosome name.
removeDupReads() supports BAM-format input and output.
New function flattenGTF() that merges overlapping features into a single interval.
New parameter for align() and subjunc(): sortReadsByCoordinates.
New parameters for featureCounts(): readShiftType, readShiftSize and additionalAttributes.
Specify strand protocol for each library individually in featureCounts().
Much improved speed of align() and subjunc().
align() and subjunc() return mapping statistics.
Default setting of buildindex() is changed to building a one-block full index.