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(v3.2.1ggplot2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