一、BSgenome和BSgenome数据包
Bioconductor提供了某些物种的全基因组序列数据包,这些数据包是基于Biostrings构建的,称为BSgenome数据包。不同物种的BSgenome数据包都有类似的数据结构,可以用统一的方式进行处理。但是BSgenome数据包仅包含有数据,它们的处理的方法由另外一个软件包提供,即BSgenome包。先安装BSgenome包(如果没有安装):
library(BiocInstaller) biocLite("BSgenome")载入BSgenome包,并查看当前版本提供的BSgenome数据包:
library(BSgenome) (ag <- available.genomes())
## [1] "BSgenome.Alyrata.JGI.v1" ## [2] "BSgenome.Amellifera.BeeBase.assembly4" ## [3] "BSgenome.Amellifera.UCSC.apiMel2" ## [4] "BSgenome.Athaliana.TAIR.04232008" ## [5] "BSgenome.Athaliana.TAIR.TAIR9" ## [6] "BSgenome.Btaurus.UCSC.bosTau3" ## [7] "BSgenome.Btaurus.UCSC.bosTau4" ## [8] "BSgenome.Btaurus.UCSC.bosTau6" ## [9] "BSgenome.Celegans.UCSC.ce10" ## [10] "BSgenome.Celegans.UCSC.ce2" ## [11] "BSgenome.Celegans.UCSC.ce6" ## [12] "BSgenome.Cfamiliaris.UCSC.canFam2" ## [13] "BSgenome.Cfamiliaris.UCSC.canFam3" ## [14] "BSgenome.Dmelanogaster.UCSC.dm2" ## [15] "BSgenome.Dmelanogaster.UCSC.dm3" ## [16] "BSgenome.Drerio.UCSC.danRer5" ## [17] "BSgenome.Drerio.UCSC.danRer6" ## [18] "BSgenome.Drerio.UCSC.danRer7" ## [19] "BSgenome.Ecoli.NCBI.20080805" ## [20] "BSgenome.Gaculeatus.UCSC.gasAcu1" ## [21] "BSgenome.Ggallus.UCSC.galGal3" ## [22] "BSgenome.Ggallus.UCSC.galGal4" ## [23] "BSgenome.Hsapiens.UCSC.hg17" ## [24] "BSgenome.Hsapiens.UCSC.hg18" ## [25] "BSgenome.Hsapiens.UCSC.hg19" ## [26] "BSgenome.Mmulatta.UCSC.rheMac2" ## [27] "BSgenome.Mmusculus.UCSC.mm10" ## [28] "BSgenome.Mmusculus.UCSC.mm8" ## [29] "BSgenome.Mmusculus.UCSC.mm9" ## [30] "BSgenome.Ptroglodytes.UCSC.panTro2" ## [31] "BSgenome.Ptroglodytes.UCSC.panTro3" ## [32] "BSgenome.Rnorvegicus.UCSC.rn4" ## [33] "BSgenome.Rnorvegicus.UCSC.rn5" ## [34] "BSgenome.Scerevisiae.UCSC.sacCer1" ## [35] "BSgenome.Scerevisiae.UCSC.sacCer2" ## [36] "BSgenome.Scerevisiae.UCSC.sacCer3" ## [37] "BSgenome.Tgondii.ToxoDB.7.0"