📄
Guide to RNA-seq Analysis
  • Introduction
  • Preparations
    • Work environment
    • Softwares and databases
    • Obtain sequencing data
    • R packages
  • Raw read processing
    • QC & trimming
    • Mapping & quantification
      • Alignment-free method
      • Alignment-based method
  • Differential expression analysis in R
    • Building a TxDb object
    • About tximport
    • Convert Salmon output to Sleuth-compatible format
    • Differential gene expression (DGE) analysis using DESeq2
      • DGE analysis with Salmon/Kallisto input
      • DGE analysis with STAR input
      • DGE analysis with STAR + RSEM input
    • Differential transcript expression (DTE) analysis using DESeq2
      • DTE analysis with Salmon/Kallisto input
      • DTE analysis with STAR + RSEM input
    • DGE and DTE analysis of Salmon/Kallisto inputs using Sleuth
    • Differential transcript usage (DTU) analysis
      • DTU analysis using DRIMSeq
      • DTU analysis using DEXSeq
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On this page
  • List of R packages used
  • CRAN
  • Bioconductor
  • GitHub

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  1. Preparations

R packages

List of R packages used

CRAN

  • data.table: https://cran.r-project.org/package=data.table

  • dplyr: https://cran.r-project.org/package=dplyr

  • reshape2: https://cran.r-project.org/package=reshape2

  • ggplot2: https://cran.r-project.org/package=ggplot2

  • ggrepel: https://cran.r-project.org/package=ggrepel

  • ggbeeswarm: https://cran.r-project.org/package=ggbeeswarm

Bioconductor

  • GenomicFeatures: https://bioconductor.org/packages/GenomicFeatures/

  • tximport: https://bioconductor.org/packages/tximport/

  • DESeq2: https://bioconductor.org/packages/DESeq2/

  • apeglm: https://bioconductor.org/packages/apeglm/

  • EnhancedVolcano: https://bioconductor.org/packages/EnhancedVolcano/

  • DRIMSeq: https://bioconductor.org/packages/DRIMSeq/

  • DEXSeq: https://bioconductor.org/packages/DEXSeq/

  • stageR: https://www.bioconductor.org/packages/stageR/

  • edgeR: https://www.bioconductor.org/packages/edgeR/

GitHub

  • wasabi: https://github.com/COMBINE-lab/wasabi

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("devtools")    # only if devtools not yet installed
BiocManager::install("COMBINE-lab/wasabi")

  • sleuth: https://github.com/pachterlab/sleuth

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("devtools")    # only if devtools not yet installed
BiocManager::install("pachterlab/sleuth")
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Last updated 5 years ago

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