Changes in version 2.2.0                        

    o   
	Improve cellCounts() on the identification of cell barcodes
	arising from ambient RNAs.

                        Changes in version 2.0.0                        

    o   
	Rsubread package is ported to Windows OS.

    o   
	New function cellCounts(): generate UMI counts for Chromium 10X
	single-cell RNA-seq data.

    o   
	flattenGTF() function can merge or chop overlap features.

    o   
	Check and display the amount of memory available on the
	computer before starting read mapping.

    o   
	Optimize the data structure used in buildindex() function to
	reduce its memory use.

    o   
	qualityScores() function can optionally retrieve quality scores
	from all the reads.

    o   
	File paths included in column names of objects returned by
	featureCounts(), align(), subjunc() and propmapped() functions
	are removed or shortened where appropriate.

    o   
	featureCounts() will be terminated if both single-end and
	paired-end reads are found in the same input file.

    o   
	Limit on the length of input file names is increased to 1000
	bytes for all functions.

                       Changes in version 1.34.0                        

    o   
	New functions: simReads() and scanFasta(). simReads() generates
	simulation RNA-seq reads for transcripts.

    o   
	align() and subjunc() estimate fragment length from mapped read
	pairs and use the estimated length to assist reporting the best
	alignment.

    o   
	align() and subjunc() prefer alignments with no indels included
	over indel-containing alignments when same number of matched
	bases are found.

    o   
	align() and subjunc() check if index files were successfully
	loaded before starting read mapping.

    o   
	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.

    o   
	buildindex(), align() and subjunc() support gzipped FASTA
	format.

    o   
	featureCounts() allows mapped reads to have ‘*’ as their
	chromosome name.

    o   
	removeDupReads() supports BAM-format input and output.

                       Changes in version 1.32.0                        

    o   
	New function flattenGTF() that merges overlapping features into
	a single interval.

    o   
	New parameter for align() and subjunc():
	sortReadsByCoordinates.

    o   
	New parameters for featureCounts(): readShiftType,
	readShiftSize and additionalAttributes.

    o   
	Specify strand protocol for each library individually in
	featureCounts().

    o   
	Much improved speed of align() and subjunc().

    o   
	align() and subjunc() return mapping statistics.

    o   
	Default setting of buildindex() is changed to building a
	one-block full index.