引用程序和文献转录组分析模块,均源于该领域公开发表文献中,广受认可的算法和开源程序。 详细信息,参考软件内置模块帮助文档,或点击在线帮助文档,进行查看。 简介如下所示: 1、原始数据碱基分布图和质量分布图 FASTX-Toolkit v0.0.13(http://hannonlab.cshl.edu/fastx_toolkit/) 2、原始数据质控 Trimmomatic v0.32 ( http://www.usadellab.org/cms/index.php?page=trimmomatic ) Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170. 3、RSEM表达量计算(Transcripts Based) Bowtie-0.12.7(http://bowtie-bio.sourceforge.net/index.shtml) Bowtie2-2.1.0(http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) RSEM-1.2.26(http://deweylab.github.io/RSEM/) Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359. Bo Li and Colin N Dewey. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics201112:323. 4、eXpress表达量计算(Transcripts Based) Bowtie-0.12.7(http://bowtie-bio.sourceforge.net/index.shtml) Bowtie2-2.1.0(http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) eXpress-1.5.1(http://bio.math.berkeley.edu/eXpress/) Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25. Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359. Roberts A and Pachter L (2012). Streaming fragment assignment for real-time analysis of sequencing experiments. Nature Methods. 5、 差异表达分析 R语言(v3.2.1)edgeR包(v3.10.2)(http://bioconductor.org/packages/release/bioc/html/edgeR.html) R语言(v3.2.1)DESeq2包(v1.8.1)(http://bioconductor.org/packages/release/bioc/html/DESeq2.html) R语言(v3.2.1)limma包(v3.24.14)(http://bioconductor.org/packages/release/bioc/html/limma.html) Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. Michael I Love, Wolfgang Huber and Simon Anders (2014): Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biology. Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43(7), e47. 6、TMM方法标准化Count数据 R语言(v3.2.1)edgeR包(v3.10.2)(http://bioconductor.org/packages/release/bioc/html/edgeR.html) Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. 7、PCA分析和作图 R语言(v3.2.1)中的PCA统计和分析函数 8、 PCoA分析和作图 R语言(v3.2.1)中的PCoA统计和分析函数 9、相关性系数计算和作图 R语言(v3.2.1)进行相关性系数分析、聚类分析和作图(cor、hclust) 10、距离矩阵计算 R语言(v3.2.1)进行距离矩阵的运算(dist) 11、距离矩阵热图 R语言(v3.2.1)进行距离矩阵的可视化作图 12、FPKM分布曲线 R语言(v3.2.1)进行密度曲线的计算和绘制(density) 13、差异基因热图 R语言(v3.2.1)中的cor函数进行相关系数计算,dist函数进行距离计算,hclust函数进行样品和基因间的聚类 14、FPKM箱线图 R语言(v3.2.1)ggplot2包(v2.2.1)中的boxplot相关功能进行盒形图的绘制 15、维恩图 R语言(v3.2.1)进行维恩图的绘制 16、 差异基因子表达模式分析 R语言(v3.2.1)中的kmeans函数进行k-means聚类,cor函数进行相关系数计算,dist函数进行距离计算,hclust函数进行差异基因间的层次聚类,cutree函数进行层次聚类结果的划分 17、差异基因子表达模式网络图 R语言(v3.2.1)Hmisc包(v3.16-0)中的rcorr函数进行相关性检验,根据检验p值和相关性系数确定基因间的连通性 18、基因调控网络图 R语言(v3.2.1)Hmisc包(v3.16-0)中的rcorr函数进行相关性检验,根据检验p值和相关性系数确定基因间的连通性 19、差异基因GO注释 goatools v0.5.7(https://github.com/tanghaibao/goatools/) Haibao Tang et al. (2015). GOATOOLS: Tools for Gene Ontology. Zenodo. 10.5281/zenodo.31628. 20、差异基因GO富集分析 goatools v0.5.7(https://github.com/tanghaibao/goatools/) Haibao Tang et al. (2015). GOATOOLS: Tools for Gene Ontology. Zenodo. 10.5281/zenodo.31628. 21、差异基因GO富集结果散点图 R语言(v3.2.1)ggplot2包(v2.2.1)中的geom_point相关功能进行GO富集散点图的绘制 22、差异基因GO富集结果柱状图 R语言(v3.2.1)ggplot2包(v2.2.1)中的geom_bar相关功能进行GO富集柱状图的绘制 23、富集GO节点有向无环图 goatools v0.5.7(https://github.com/tanghaibao/goatools/) Haibao Tang et al. (2015). GOATOOLS: Tools for Gene Ontology. Zenodo. 10.5281/zenodo.31628. 24、差异基因KEGG注释 KOBAS v2.0-20150126(http://kobas.cbi.pku.edu.cn) Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C. and Wei, L. (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res, 39, W316-322. 25、差异基因KEGG富集分析 KOBAS v2.0-20150126(http://kobas.cbi.pku.edu.cn) Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., Kong, L., Gao, G., Li, C. and Wei, L. (2011) KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res, 39, W316-322. 26、差异基因KEGG富集结果散点图 R语言(v3.2.1)ggplot2包(v2.2.1)中的geom_point相关功能进行KEGG富集散点图的绘制
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