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生信 同时为方便大家自己分析转录组数据，我们也正在翻译 RNA-seq Data Analysis A Practical Approach（目录参见此文：RNA-seq数据分析实用方法）这本书，供大家入门使用。目前翻译工作正在进行中，预期月底完成初稿。此书目前还剩余以下章节需要翻译，希望熟悉此领域的给小编留言，加入我们翻译团队。 5.4 MAPPING-BASED ASSEMBLY 95 5.4.1 Cufflinks 95 5.4.2 Scripture 97 5.5 DE NOVO ASSEMBLY 98 5.5.1 Velvet + Oases 98 5.5.2 Trinity 100 5.6 SUMMARY 104 6.3 QUANTITATION OF GENE EXPRESSION 116 6.3.1 Counting Reads per Genes 117 6.3.1.1 HTSeq 117 6.3.2 Counting Reads per Transcripts 120 6.3.2.1 Cufflinks 122 6.3.2.2 eXpress 122 6.3.3 Counting Reads per Exons 126 8.1 INTRODUCTION 147 8.2 TECHNICAL VS. BIOLOGICAL REPLICATES 148 8.3 STATISTICAL DISTRIBUTIONS IN RNA-SEQ DATA 149 8.3.1 Biological Replication, Count Distributions, and Choice of Software 150 8.4 NORMALIZATION 152 8.5.7 For Reference: Code Examples for Other Bioconductor Packages 168 8.5.8 Limma 169 8.5.9 SAMSeq (samr package) 170 8.5.10 edgeR 171 8.5.11 DESeq2 Code Example for a Multifactorial Experiment 171 8.5.12 For Reference: edgeR Code Example 174 8.5.13 Limma Code Example 175 Chapter 9 ◾ Analysis of Differential Exon Usage 181 9.1 INTRODUCTION 181 9.2 PREPARING THE INPUT FILES FOR DEXSeq 183 9.3 READING DATA IN TO R 184 9.4 ACCESSING THE ExonCountSet OBJECT 185 9.5 NORMALIZATION AND ESTIMATION OF THE VARIANCE 187 9.6 TEST FOR DIFFERENTIAL EXON USAGE 190 9.7 VISUALIZATION 193 9.8 SUMMARY 198 13.1 INTRODUCTION 259 13.2 DISCOVERY OF SMALL RNAs—miRDeep2 260 13.2.1 GFF files 260 13.2.2 FASTA Files of Known miRNAs 263 13.2.3 Setting up the Run Environment 263 13.2.4 Running miRDeep2 266 13.2.4.1 miRDeep2 Output 266 13.3 miRANALYZER 268 13.3.1 Running miRanalyzer 271 13.4 miRNA TARGET ANALYSIS 271 13.4.1 Computational Prediction Methods 272 13.4.2 Artificial Intelligence Methods 274 13.4.3 Experimental Support-Based Methods 275 |
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