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将生成一个纸样scRNA-seq样本包含的数据,基于样本指数集名称由用户提供。返回的列表对象结构cellCounts()也简化了。cellCounts()现在也输出文件和一个gzip的BAM FASTQ文件为每个样本包括生读。版本变化2.2.0 o提高cellCounts()引起的细胞识别的条形码环境rna。变化在2.0.0版本中o Rsubread包被移植到Windows操作系统。o新函数cellCounts():为铬生成UMI数10 x单细胞RNA-seq数据。o flattenGTF()函数可以合并或砍重叠功能。 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.