Changes in version 2.16.0
o
Add support for ARM64 platforms.
o
Add support for CBCL format in cellCounts.
Changes in version 2.12.0
o
Improve the data structure used by cellCounts to further
improve its speed.
o
More checks for input parameters to prevent cellCounts from
crashing.
o
Improve the screen output of cellCounts.
Changes in version 2.10.0
o
Added inbuilt RefSeq annotation for mm39 (mouse genome Build
39).
o
Streamlined the mapping and counting processes in cellCounts.
o
Added support for processing dual-index 10x data in cellCounts.
Changes in version 2.6.0
o
Improved the speed of cellCounts and also reduced its memory
use.
o
Added a parameter 'umi.cutoff' to cellCounts to call all the
cells that had a total UMI count greater than the specified
threshold.
o
Added support for FASTQ-format read input in CellCounts.
Changes in version 2.4.0
o
The 'isPairedEnd' parameter in featureCounts() is now used to
check if the type of input reads (paired-end or single-end) is
correctly specified.
o
A new parameter 'countReadPairs' was added to featureCounts to
specify if read pairs should be counted for paired-end read
data.
o
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.
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.