内容

1介绍

可变聚腺苷酸化(APA)是最重要的一个普遍的人类基因转录后调控机制。像可变剪接,APA可以创建蛋白质组多样性。此外,它定义了3 ' UTR和结果改变基因的表达。它是一个严格控制的过程和监管不力一样APA可导致细胞病理效应,如不受控制的细胞周期和增长。虽然开发了几种高通量测序方法,仍有有限的数据可用。

RNA-seq已经成为最常用的方法量化全基因组基因表达。有大量RNA-seq数据集在公共数据库如地理和TCGA可用。出于这个原因,我们从传统发展InPAS算法识别APA RNA-seq数据。

InPAS的工作流程是:

2如何

首先,InPAS负载所需的库,物种特定BSgenome, TxDb如下。

库(InPAS)库(BSgenome.Mmusculus.UCSC.mm10)图书馆(TxDb.Mmusculus.UCSC.mm10.knownGene)路径< file.path (find.package (“InPAS”)、“extdata”)

接下来,准备使用功能注释utr3AnnotationTxDb和org注释。请注意,3 ' UTR注释准备的utr3Annotation包括下一个带注释的地区差距。

库(org.Hs.eg.db) samplefile < -系统。文件(“extdata”、“hg19_knownGene_sample。sqlite”,包= " GenomicFeatures”) txdb < - loadDb utr3.sample (samplefile)。庵野< - utr3Annotation (txdb = txdb orgDbSYMBOL =“org.Hs.egSYMBOL”) utr3.sample.anno
与155年# #农庄对象范围和7元数据列:# # seqnames范围链|特性# # < Rle > < IRanges > < Rle > | <人物> # # uc001bum。2 _5 | IQCC | utr3 chr1 32673684 - 32673684 + | utr3 # # uc001fbq。3_3|S100A9|utr3 chr1 153333315-153333503 + | utr3 ## uc001gde.2_2|LRRC52|utr3 chr1 165533062-165533185 + | utr3 ## uc001hfg.3_15|PFKFB2|utr3 chr1 207245717-207251162 + | utr3 ## uc001hfh.3_15|PFKFB2|utr3 chr1 207252365-207254368 + | utr3 ## ... ... ... ... . ... ## uc004dsv.3_19|PHF8|CDS chrX 53964414-53964492 - | CDS ## uc004dsx.3_15|PHF8|CDS chrX 53969797-53969835 - | CDS ## uc004ehz.1_5|ARMCX3|CDS chrX 100879970-100881109 + | CDS ## uc004elw.3_6|FAM199X|CDS chrX 103434289-103434459 + | CDS ## uc004fmj.1_10|GAB3|CDS chrX 153906455-153906571 - | CDS ## annotatedProximalCP exon transcript ##    ## uc001bum.2_5|IQCC|utr3 unknown uc001bum.2_5 uc001bum.2 ## uc001fbq.3_3|S100A9|utr3 unknown uc001fbq.3_3 uc001fbq.3 ## uc001gde.2_2|LRRC52|utr3 unknown uc001gde.2_2 uc001gde.2 ## uc001hfg.3_15|PFKFB2|utr3 unknown uc001hfg.3_15 uc001hfg.3 ## uc001hfh.3_15|PFKFB2|utr3 unknown uc001hfh.3_15 uc001hfh.3 ## ... ... ... ... ## uc004dsv.3_19|PHF8|CDS unknown uc004dsv.3_19 uc004dsv.3 ## uc004dsx.3_15|PHF8|CDS unknown uc004dsx.3_15 uc004dsx.3 ## uc004ehz.1_5|ARMCX3|CDS unknown uc004ehz.1_5 uc004ehz.1 ## uc004elw.3_6|FAM199X|CDS unknown uc004elw.3_6 uc004elw.3 ## uc004fmj.1_10|GAB3|CDS unknown uc004fmj.1_10 uc004fmj.1 ## gene symbol truncated ##    ## uc001bum.2_5|IQCC|utr3 55721 IQCC FALSE ## uc001fbq.3_3|S100A9|utr3 6280 S100A9 FALSE ## uc001gde.2_2|LRRC52|utr3 440699 LRRC52 FALSE ## uc001hfg.3_15|PFKFB2|utr3 5208 PFKFB2 FALSE ## uc001hfh.3_15|PFKFB2|utr3 5208 PFKFB2 FALSE ## ... ... ... ... ## uc004dsv.3_19|PHF8|CDS 23133 PHF8 FALSE ## uc004dsx.3_15|PHF8|CDS 23133 PHF8 FALSE ## uc004ehz.1_5|ARMCX3|CDS 51566 ARMCX3 FALSE ## uc004elw.3_6|FAM199X|CDS 139231 FAM199X FALSE ## uc004fmj.1_10|GAB3|CDS 139716 GAB3 FALSE ## ------- ## seqinfo: 27 sequences from hg19 genome; no seqlengths

用户还可以直接加载3 ' UTR注释中包含这个包mm10和hg19。这里我们展示如何加载预构建mm10 3 ' UTR注释文件。

# # # step1注释从数据集数据负载(utr3.mm10)

覆盖率计算,需要对齐BEDGraph格式的文件,可以从BAM生成文件使用genomecov工具与参数:bedtools bg分裂。覆盖率数据的潜在pA网站确认可以使用提供的分类器过滤/调整cleanUpdTseq。下面的脚本说明所需的函数调用执行完整的分析使用InPAS。

负载(文件。路径(路径,“polyA.rds”))图书馆(cleanUpdTSeq)数据(分类)bedgraphs < - c(文件。路径(路径、“Baf3.extract.bedgraph”)文件。路径(路径,“UM15.extract.bedgraph”)) hugeData < -假# # step1计算覆盖范围< - coverageFromBedGraph (bedgraphs、标签= c (“Baf3”、“UM15”),基因组= BSgenome.Mmusculus.UCSC。mm10 hugeData = hugeData) # #我们希望覆盖率应大于0.75的表达基因。# #因为演示数据用于基因组的一个子集。coverageRate(覆盖率=覆盖率,txdb = TxDb.Mmusculus.UCSC.mm10。= BSgenome.Mmusculus.UCSC knownGene,基因组。=农庄mm10 (“chr6范围= IRanges (98013000, 98013000)))
# #链信息将被忽略。
# # gene.coverage。expressed.gene.coverage率。UTR3.coverage率。率# # Baf3 0.01031381 0.6300834 0.01830495 # # UM15 0.01020966 0.6236834 0.01846496 # # UTR3.expressed.gene.subset.coverage。率0.8082201 # # # # Baf3 UM15 0.8152853
# #步骤2预测乳沟网站CPs < - CPsites(覆盖率=覆盖基因组= BSgenome.Mmusculus.UCSC。mm10 utr3 = utr3。mm10 search_point_START = 200, cutEnd =。2, long_coverage_threshold=3, background="10K", txdb=TxDb.Mmusculus.UCSC.mm10.knownGene, PolyA_PWM=pwm, classifier=classifier, shift_range=50, step=10) head(CPs)
与4 # #农庄对象范围和12元数据列:# # seqnames范围链| # # < Rle > < IRanges > < Rle > | # # uc009daz。2 _10 | Mitf | utr3 chr6 98018176 - 98018176 + | # # uc009dhz。2_19|Atg7|utr3 chr6 114859343-114860614 + | ## uc009dmb.2_4|Lrtm2|utr3 chr6 119315133-119317055 - | ## uc009eet.1_3|BC035044|utr3 chr6 128848044-128850081 - | ## annotatedProximalCP exon transcript ##    ## uc009daz.2_10|Mitf|utr3 unknown uc009daz.2_10 uc009daz.2 ## uc009dhz.2_19|Atg7|utr3 unknown uc009dhz.2_19 uc009dhz.2 ## uc009dmb.2_4|Lrtm2|utr3 unknown uc009dmb.2_4 uc009dmb.2 ## uc009eet.1_3|BC035044|utr3 unknown uc009eet.1_3 uc009eet.1 ## gene symbol truncated fit_value ##     ## uc009daz.2_10|Mitf|utr3 17342 Mitf FALSE 12594.674 ## uc009dhz.2_19|Atg7|utr3 74244 Atg7 FALSE 27383.413 ## uc009dmb.2_4|Lrtm2|utr3 211187 Lrtm2 FALSE 168.551 ## uc009eet.1_3|BC035044|utr3 232406 BC035044 FALSE 123.974 ## Predicted_Proximal_APA Predicted_Distal_APA ##   ## uc009daz.2_10|Mitf|utr3 98018978 98021358 ## uc009dhz.2_19|Atg7|utr3 114859674 114862071 ## uc009dmb.2_4|Lrtm2|utr3 119316541 119315133 ## uc009eet.1_3|BC035044|utr3 128849177 128846744 ## type utr3start utr3end ##    ## uc009daz.2_10|Mitf|utr3 novel proximal 98018276 98021358 ## uc009dhz.2_19|Atg7|utr3 novel distal 114859443 114860614 ## uc009dmb.2_4|Lrtm2|utr3 novel proximal 119316955 119315133 ## uc009eet.1_3|BC035044|utr3 novel distal 128849981 128848044 ## ------- ## seqinfo: 42 sequences from mm10 genome; no seqlengths
# # step3估计3 utr使用res < - testUsage (CPsites = CPs,覆盖率=覆盖率,基因组= BSgenome.Mmusculus.UCSC。mm10 utr3 = utr3。费舍尔mm10、方法= "。准确”,gp1中= " Baf3”, gp2 = " UM15”) # # step4查看结果(res,“农庄”)
与4 # #农庄对象范围和27元数据列:# # seqnames范围链| annotatedProximalCP # # < Rle > < IRanges > < Rle > | <人物> # # uc009daz。2 chr6 98018176 - 98018176 + | # # uc009dhz不明。2chr6 114859343-114862071 + | unknown ## uc009dmb.2 chr6 119315133-119317055 - | unknown ## uc009eet.1 chr6 128846744-128850081 - | unknown ## transcript gene symbol truncated fit_value ##      ## uc009daz.2 uc009daz.2 17342 Mitf FALSE 12594.674 ## uc009dhz.2 uc009dhz.2 74244 Atg7 FALSE 27383.413 ## uc009dmb.2 uc009dmb.2 211187 Lrtm2 FALSE 168.551 ## uc009eet.1 uc009eet.1 232406 BC035044 FALSE 123.974 ## Predicted_Proximal_APA Predicted_Distal_APA type ##    ## uc009daz.2 98018978 98021358 novel proximal ## uc009dhz.2 114859674 114862071 novel distal ## uc009dmb.2 119316541 119315133 novel proximal ## uc009eet.1 128849177 128846744 novel distal ## utr3start utr3end Baf3_short.form.usage UM15_short.form.usage ##     ## uc009daz.2 98018276 98021358 33.53134 1.05215 ## uc009dhz.2 114859443 114860614 520.91479 172.15235 ## uc009dmb.2 119316955 119315133 8.85786 49.53562 ## uc009eet.1 128849981 128848044 21.64617 0.00000 ## Baf3_long.form.usage UM15_long.form.usage Baf3_PDUI UM15_PDUI ##     ## uc009daz.2 282.82402 189.1411 0.894007 0.994468 ## uc009dhz.2 208.02460 456.5446 0.285380 0.726176 ## uc009dmb.2 8.53513 70.8126 0.490722 0.588398 ## uc009eet.1 8.90222 23.2913 0.291414 1.000000 ## short.mean.gp1 long.mean.gp1 short.mean.gp2 long.mean.gp2 ##     ## uc009daz.2 33.53134 282.82402 1.05215 189.1411 ## uc009dhz.2 520.91479 208.02460 172.15235 456.5446 ## uc009dmb.2 8.85786 8.53513 49.53562 70.8126 ## uc009eet.1 21.64617 8.90222 0.00000 23.2913 ## PDUI.gp1 PDUI.gp2 dPDUI logFC P.Value adj.P.Val ##       ## uc009daz.2 0.894007 0.994468 -0.1004606 -0.153638 1.58698e-06 2.11597e-06 ## uc009dhz.2 0.285380 0.726176 -0.4407961 -1.347436 1.70948e-60 6.83790e-60 ## uc009dmb.2 0.490722 0.588398 -0.0976754 -0.261885 5.93031e-01 5.93031e-01 ## uc009eet.1 0.291414 1.000000 -0.7085863 -1.778859 4.13501e-08 8.27003e-08 ## ------- ## seqinfo: 1 sequence from an unspecified genome; no seqlengths
filterRes (res gp1中=“Baf3 gp2 =“UM15 background_coverage_threshold = 3, adj.P.Val_cutoff = 0.05, dPDUI_cutoff = 0.3, PDUI_logFC_cutoff = 0.59)
与4 # #农庄对象范围和28元数据列:# # seqnames范围链| annotatedProximalCP # # < Rle > < IRanges > < Rle > | <人物> # # uc009daz。2 chr6 98018176 - 98018176 + | # # uc009dhz不明。2chr6 114859343-114862071 + | unknown ## uc009dmb.2 chr6 119315133-119317055 - | unknown ## uc009eet.1 chr6 128846744-128850081 - | unknown ## transcript gene symbol truncated fit_value ##      ## uc009daz.2 uc009daz.2 17342 Mitf FALSE 12594.674 ## uc009dhz.2 uc009dhz.2 74244 Atg7 FALSE 27383.413 ## uc009dmb.2 uc009dmb.2 211187 Lrtm2 FALSE 168.551 ## uc009eet.1 uc009eet.1 232406 BC035044 FALSE 123.974 ## Predicted_Proximal_APA Predicted_Distal_APA type ##    ## uc009daz.2 98018978 98021358 novel proximal ## uc009dhz.2 114859674 114862071 novel distal ## uc009dmb.2 119316541 119315133 novel proximal ## uc009eet.1 128849177 128846744 novel distal ## utr3start utr3end Baf3_short.form.usage UM15_short.form.usage ##     ## uc009daz.2 98018276 98021358 33.53134 1.05215 ## uc009dhz.2 114859443 114860614 520.91479 172.15235 ## uc009dmb.2 119316955 119315133 8.85786 49.53562 ## uc009eet.1 128849981 128848044 21.64617 0.00000 ## Baf3_long.form.usage UM15_long.form.usage Baf3_PDUI UM15_PDUI ##     ## uc009daz.2 282.82402 189.1411 0.894007 0.994468 ## uc009dhz.2 208.02460 456.5446 0.285380 0.726176 ## uc009dmb.2 8.53513 70.8126 0.490722 0.588398 ## uc009eet.1 8.90222 23.2913 0.291414 1.000000 ## short.mean.gp1 long.mean.gp1 short.mean.gp2 long.mean.gp2 ##     ## uc009daz.2 33.53134 282.82402 1.05215 189.1411 ## uc009dhz.2 520.91479 208.02460 172.15235 456.5446 ## uc009dmb.2 8.85786 8.53513 49.53562 70.8126 ## uc009eet.1 21.64617 8.90222 0.00000 23.2913 ## PDUI.gp1 PDUI.gp2 dPDUI logFC P.Value adj.P.Val ##       ## uc009daz.2 0.894007 0.994468 -0.1004606 -0.153638 1.58698e-06 2.11597e-06 ## uc009dhz.2 0.285380 0.726176 -0.4407961 -1.347436 1.70948e-60 6.83790e-60 ## uc009dmb.2 0.490722 0.588398 -0.0976754 -0.261885 5.93031e-01 5.93031e-01 ## uc009eet.1 0.291414 1.000000 -0.7085863 -1.778859 4.13501e-08 8.27003e-08 ## PASS ##  ## uc009daz.2 FALSE ## uc009dhz.2 TRUE ## uc009dmb.2 FALSE ## uc009eet.1 TRUE ## ------- ## seqinfo: 1 sequence from an unspecified genome; no seqlengths

上述步骤可以通过一个函数调用。

如果(互动()){res < inPAS (bedgraphs = bedgraphs标签= c (“Baf3”、“UM15”),基因组= BSgenome.Mmusculus.UCSC。mm10 utr3 = utr3。mm10 gp1中=“Baf3 gp2 =“UM15 txdb = TxDb.Mmusculus.UCSC.mm10。knownGene search_point_START = 200, short_coverage_threshold = 15, long_coverage_threshold = 3, cutStart = 0, cutEnd =。2 hugeData = FALSE shift_range = 50, PolyA_PWM = pwm,分类器=分类器方法= "费舍尔。准确”,adj.P.Val_cutoff = 0.05, dPDUI_cutoff = 0.3, PDUI_logFC_cutoff = 0.59)}

InPAS还可以处理一组数据。

inPAS (bedgraphs = bedgraphs[1],标签= c (“Baf3”),基因组= BSgenome.Mmusculus.UCSC。mm10 utr3 = utr3。mm10 gp1中=“Baf3 gp2 = NULL, txdb = TxDb.Mmusculus.UCSC.mm10。knownGene search_point_START = 200, short_coverage_threshold = 15, long_coverage_threshold = 3, cutStart = 0, cutEnd =。2 hugeData = FALSE PolyA_PWM = pwm,分类器=分类器方法=“singleSample adj.P.Val_cutoff = 0.05, = 10步)
在迭代1 # #聚合logLik: -1835.501 # #聚集在迭代5 logLik: -838.8306 # #聚集在迭代1 logLik: -1496.738 # #聚集在迭代13 logLik: -724.6964 # #聚集在迭代1 logLik: -997.3022 # #聚集在迭代7 logLik: -555.5656 # #聚集在迭代1 logLik: -188.938 # #聚集在迭代23 logLik: -152.6663 # #聚集在迭代1 logLik: -462.3804 # #聚合与logLik迭代10:-214.1651
# # dPDUI gp2 - gp1中计算。
与6 # #农庄对象范围和22元数据列:# # seqnames范围链| annotatedProximalCP # # < Rle > < IRanges > < Rle > | <人物> # # uc009daz。2 chr6 98018176 - 98018176 + | # # uc009dhz不明。2chr6 114859343-114862075 + | unknown ## uc009die.2 chr6 114860617-114862164 - | unknown ## uc009dmb.2 chr6 119315133-119317055 - | unknown ## uc009eet.1 chr6 128847265-128850081 - | unknown ## uc009eol.1 chr6 140651362-140651622 + | unknown ## transcript gene symbol truncated fit_value ##      ## uc009daz.2 uc009daz.2 17342 Mitf FALSE 17843.7079 ## uc009dhz.2 uc009dhz.2 74244 Atg7 FALSE 7630.4981 ## uc009die.2 uc009die.2 232334 Vgll4 FALSE 10704.6989 ## uc009dmb.2 uc009dmb.2 211187 Lrtm2 FALSE 18.6351 ## uc009eet.1 uc009eet.1 232406 BC035044 FALSE 227.5418 ## uc009eol.1 uc009eol.1 11569 Aebp2 TRUE 204539.6984 ## Predicted_Proximal_APA Predicted_Distal_APA type ##    ## uc009daz.2 98019022 98021358 novel proximal ## uc009dhz.2 114860283 114862075 novel distal ## uc009die.2 114861446 114860617 novel distal ## uc009dmb.2 119316683 119315133 novel proximal ## uc009eet.1 128848843 128847265 novel distal ## uc009eol.1 140651566 140651622 novel proximal ## utr3start utr3end data2 Baf3_short.form.usage ##     ## uc009daz.2 98018176 98021358 473,460,457,... 29.66026 ## uc009dhz.2 114859343 114860614 184,184,184,... 3.72545 ## uc009die.2 114862164 114862092 76,76,76,... 121.88814 ## uc009dmb.2 119317055 119315133 11,12,12,... 9.22610 ## uc009eet.1 128850081 128848044 22,22,22,... 22.04495 ## uc009eol.1 140651362 140651622 1408,1412,1384,... 1065.98013 ## Baf3_long.form.usage Baf3_PDUI short.mean long.mean PDUI ##      ## uc009daz.2 283.38939 0.905254 29.6603 283.389 0.905254 ## uc009dhz.2 209.97881 0.982567 3.72545 209.979 0.982567 ## uc009die.2 174.12289 0.588231 121.888 174.123 0.588231 ## uc009dmb.2 9.11799 0.497053 9.2261 9.11799 0.497053 ## uc009eet.1 10.32742 0.319020 22.045 10.3274 0.31902 ## uc009eol.1 221.45614 0.172013 1065.98 221.456 0.172013 ## P.Value adj.P.Val dPDUI PASS ##     ## uc009daz.2 1 1 NaN FALSE ## uc009dhz.2 1 1 NaN FALSE ## uc009die.2 1 1 NaN FALSE ## uc009dmb.2 1 1 NaN FALSE ## uc009eet.1 1 1 NaN FALSE ## uc009eol.1 1 1 NaN FALSE ## ------- ## seqinfo: 1 sequence from an unspecified genome; no seqlengths

3会话信息

sessionInfo ()

R版本4.0.3(2020-10-10)平台:x86_64-pc-linux-gnu(64位)下运行:Ubuntu 18.04.5 LTS

矩阵产品:默认布拉斯特区:/home/biocbuild/bbs - 3.12 - bioc / R / lib / libRblas。所以LAPACK: /home/biocbuild/bbs - 3.12 - bioc / R / lib / libRlapack.so

地区:[1]LC_CTYPE = en_US。utf - 8 LC_NUMERIC = C
[3]而= en_US。utf - 8 LC_COLLATE = C
[5]LC_MONETARY = en_US。utf - 8 LC_MESSAGES = en_US.UTF-8
[7]LC_PAPER = en_US。utf - 8 LC_NAME = C
[9]LC_ADDRESS C = C LC_TELEPHONE =
[11]LC_MEASUREMENT = en_US。utf - 8 LC_IDENTIFICATION = C

附加基本包:[1]stats4并行数据图形grDevices跑龙套数据集[8]方法基础

其他附加包:[1]cleanUpdTSeq_1.28.0
[2]org.Hs.eg.db_3.12.0
[3]TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 [4] BSgenome.Mmusculus.UCSC.mm10_1.4.0
[5]BSgenome_1.58.0
[6]rtracklayer_1.50.0
[7]Biostrings_2.58.0
[8]XVector_0.30.0
[9]InPAS_1.22.0
[10]GenomicFeatures_1.42.0
[11]AnnotationDbi_1.52.0
[12]GenomicRanges_1.42.0
[13]GenomeInfoDb_1.26.0
[14]IRanges_2.24.0
[15]S4Vectors_0.28.0
[16]Biobase_2.50.0
[17]BiocGenerics_0.36.0
[18]BiocStyle_2.18.0

通过加载一个名称空间(而不是附加):[1]colorspace_1.4-1 seqinr_4.2-4
[3]ellipsis_0.3.1 class_7.3-17
[5]depmixS4_1.4-2 biovizBase_1.38.0
[7]htmlTable_2.1.0 base64enc_0.1-3
[9]dichromat_2.0-0 rstudioapi_0.11
[11]bit64_4.0.5 xml2_1.3.2
[13]splines_4.0.3 knitr_1.30
[15]ade4_1.7-15 Formula_1.2-4
[17]Rsamtools_2.6.0 cluster_2.1.0
[19]dbplyr_1.4.4 png_0.1-7
[21]BiocManager_1.30.10 compiler_4.0.3
[23]httr_1.4.2 backports_1.1.10
[25]assertthat_0.2.1 Matrix_1.2-18
[27]lazyeval_0.2.2 limma_3.46.0
[29]htmltools_0.5.0 prettyunits_1.1.1
[31]tools_4.0.3 gtable_0.3.0
[33]glue_1.4.2 GenomeInfoDbData_1.2.4
[35]dplyr_1.0.2 rappdirs_0.3.1
[37]Rcpp_1.0.5 vctrs_0.3.4
[39]preprocessCore_1.52.0 nlme_3.1 - 150
[41]xfun_0.18 stringr_1.4.0
[43]lifecycle_0.2.0 ensembldb_2.14.0
[45]xml_3.99 - 0.5 zlibbioc_1.36.0
[47]MASS_7.3-53 scales_1.1.1
[49]VariantAnnotation_1.36.0 hms_0.5.3
[51]MatrixGenerics_1.2.0 ProtGenerics_1.22.0
[53]SummarizedExperiment_1.20.0 AnnotationFilter_1.14.0
[55]RColorBrewer_1.1-2 yaml_2.2.1
[57]curl_4.3 memoise_1.1.0
[59]gridExtra_2.3 ggplot2_3.3.2
[61]biomaRt_2.46.0 rpart_4.1-15
[63]latticeExtra_0.6-29 stringi_1.5.3
[65]RSQLite_2.2.1 e1071_1.7-4
[67]checkmate_2.0.0 BiocParallel_1.24.0
[69]truncnorm_1.0-8 rlang_0.4.8
[71]pkgconfig_2.0.3 matrixStats_0.57.0
[73]bitops_1.0-6 Rsolnp_1.16
[75]evaluate_0.14 lattice_0.20-41
[77]purrr_0.3.4 GenomicAlignments_1.26.0
[79]htmlwidgets_1.5.2 bit_4.0.4
[81]tidyselect_1.1.0 magrittr_1.5
[83]bookdown_0.21 R6_2.4.1
[85]generics_0.0.2 Hmisc_4.4-1
[87]DelayedArray_0.16.0 DBI_1.1.0
[89]pillar_1.4.6 foreign_0.8 - 80
[91]BSgenome.Drerio.UCSC.danRer7_1.4.0 survival_3.2-7
[93]rcurl_1.98 - 1.2 nnet_7.3-14
[95]tibble_3.0.4 crayon_1.3.4
[97]BiocFileCache_1.14.0 rmarkdown_2.5
[99]jpeg_0.1 - 8.1 progress_1.2.2
[101]grid_4.0.3 data.table_1.13.2
[103]blob_1.2.1 digest_0.6.27
[105]openssl_1.4.3 munsell_0.5.0
[107]Gviz_1.34.0 askpass_1.1

1。谢泼德,S。劳森,n d &朱l . j .准确识别聚腺苷酸化网站从3′末端深测序使用朴素贝叶斯分类器。生物信息学29日,2564 - 2571 (2013)。