版本变化2.10.0 o添加内置RefSeq注释mm39(老鼠基因组构建39)。o流线型cellCounts映射和计算过程。o添加支持处理dual-index 10 x cellCounts中的数据。版本变化2.6.0 o提高cellCounts的速度,也减少了内存的使用。o“umi添加了一个参数。截止的cellCounts打电话给所有的细胞有一个UMI总数大于指定的阈值。o添加支持FASTQ-format CellCounts读取输入。版本变化测试盒框o ' isPairedEnd参数在featureCounts()现在是用来检查是否输入读取(paired-end或单头)的类型是正确地指定。o添加了一个新的参数的countReadPairs featureCounts指定如果读双应该paired-end读取数据。o变化的输入参数和输出cellCounts()函数。 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.