模块帮助文档

原始数据质控

• fastq数据统计　FASTQ Summary Statistics

• 原始数据碱基分布图　Draw nucleotides distribution chart

• 原始数据质量分布图　Draw quality score boxplot

• SE数据去接头、低质量　Trimmomatic SE(single-end)

• PE数据去接头、低质量　Trimmomatic PE(paired-end)

• fastq转fasta文件　Convert FASTQ to FASTA

• 计算fasta序列长度　Compute sequence length

• 按长度过滤fasta序列　ilter sequences by length

• fasta序列统计　Fasta Statistics

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I. 表达量计算（Transcripts Based）

• 构建转录本参考索引　Build Transcript Reference Index

• RSEM方法比对和表达量计算　RSEM: Align and Estimate Abundance

• eXpress方法比对和表达量计算　eXpress: Align and Estimate Abundance

• 合并多个样品RSEM表达量计算结果，得到count和fpkm矩阵　merge RSEM estimates

• 合并多个样品eXpress表达量计算结果，得到count和fpkm矩阵　merge eXpress estimates

II. 表达量计算（Ref & Annotation Based）

差异表达分析

• 差异表达分析，支持edgeR、DESeq2、limma    Differential Expression Analysis

• 过滤差异表达分析结果　Filter DE Analysis Result

• 统计差异表达分析结果　Summary DE Analysis Result

• 生成分组文件　Generate sample group file from file header

• 获得所有比较的差异基因并集列表　Retrieve All Diff Genes list

• 批处理：过滤差异表达分析结果　Batch Mode: Filter DE Analysis Result

• 批处理：获得各比较差异基因列表   Batch Mode: Retrieve Diff Genes list

矩阵操作

• 通过矩阵得到所有基因名列表　Fetch all genes(row names) list from matrix

• 根据基因列表得到对应基因的矩阵　Retrieve Rows from matrix/tabular file

• TMM方法均一化count矩阵　TMM scaling normalization for count matrix

• 矩阵数值log2变换　FPKM matrix log2 transform

• 组内样品求fpkm均值　Replicates to Sample averages

• 矩阵转置　Matrix Transpose

• 合并多个矩阵　Merge Matrices

• 按样品名列表顺序重排矩阵列顺序　Reorder Matrix columns

• 获得一个子矩阵　Get a sub-Matrix

标准分析

• 主成分分析　PCA analysis and plot PCA

• 主坐标分析　PCOA analysis and plot PCOA

• 3D散点图　3D Scatterplot

• 样品相关性系数计算　Create Sample Correlation Matrix

• 距离矩阵计算　Generate distance matrix

• 得到矩阵数值满足条件的行列信息　Retrieve pairs in Matrix

• 距离矩阵热图　Make Distance HeatMap

• 组间距离关系盒形图　Make Distance Boxplots

• 距离/相关性系数密度曲线　Make Density Plot

• 热图　Plot heatmap with tree

• 层次聚类树　Plot hcluster tree

• 画树状图　Plot Tree

• FPKM分布曲线　Plot FPKM distribution for all samples

• FPKM盒形图　FPKM Boxplot for all samples

• 两样品间FPKM散点图　FPKM Scatterplot for two samples

• 两两样品FPKM散点图　FPKM Scatterplot for all pair-wise samples

• 单个基因表达水平折线图　Matrix to gene plots

• 维恩图　Plot Venn Diagram

• 子表模式、时序分析　Subcluster Expression Analysis

• 子表达模式网络图　Plot Genes subClusters Network

• 基因调控网络图　Plot Gene Regulatory Network

GO相关分析

• 差异表达分析结果添加GO注释信息　Add GO Annotation

• GO注释结果按GO等级统计　GO level statistic about GO annotation file

• GO等级统计结果柱状图　Plot GO bar

• 根据GO注释结果，列出所有基因与GO关系　Report all input Gene -> GO Relations

• 给定GO Term，输出该GO Term下所有GO节点　Print the hierarchy below GO Term

• GO富集分析　GO Enrichment Analysis

• GO富集散点图　Plot GO Enrichment

• GO富集柱状图　GO Enrichment Bar Plot

• 统计GO富集结果　Summary GO Enrichment

• GO富集结果有向无环图　Plot Enriched GO DAG Grapth

• GO有向无环图　Plot GO lineage DAG Grapth

• 带P值的GO有向无环图　Plot GO lineage DAG Grapth with Pvalue

• 批处理：差异表达分析结果添加GO注释信息　Batch Mode: Add GO Annotation

• 批处理：GO富集分析　Batch Mode: GO Enrichment Analysis

• 批处理：GO富集散点图　Batch Mode: Plot GO Enrichment

• 批处理：GO富集柱状图　Batch Mode: GO Enrichment Bar Plot

• 批处理：GO富集结果有向无环图　Batch Mode: Plot Enriched GO DAG Grapth

KEGG相关分析

• 差异表达分析结果添加KEGG注释信息　Add KEGG Annotation

• KEGG注释文件统计　KEGG statistic about KEGG annotation file

• KEGG富集分析　KEGG Enrichment Analysis

• KEGG富集散点图　Plot KEGG Enrichment

• 统计KEGG富集结果　Summary KEGG Enrichment

• 批处理：差异表达分析结果添加KEGG注释信息　Batch Mode: Add KEGG Annotation

• 批处理：KEGG富集分析　Batch Mode: KEGG Enrichment Analysis

• 批处理：KEGG富集散点图　Batch Mode: Plot KEGG Enrichment