DESeqtools

A package for analysis of RNASeq-data based on the package DESeq2. (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)

Package installation

install.packages("devtools")
library(devtools)
devtools::install_github("SHerresthal/DESeqtools")

Example Analysis

This tutorial contains an example analysis which can be used as a template for standard bulk RNA-seq analysis using a dataset of human MDSC-like cells (published here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92852). See https://sherresthal.github.io/DESeqtools for the example workflow. It contains:

1. Installation of the DESeqtools-package
2. Project Information
3. Obligatory Data Structure
4. Data Import
5. Build DESeq Data Set
6. Exploratory Data Analysis
7. Batch Effect Removal (treat with caution!)
8. Differential expression analysis
9. Export of the results
10. Save image and session info

Changes in v002

• GSEA function: bugfix

• highestGenes:

  • Data argument flexible
  • fill of boxplots according to gene type
  • plot_title as argument

• plotSingleGene:

  • Bug fix in shape option

• plotHeatmap

  • column annotation now flexible
  • sample table now flexible

• plotGeneSetHeatmap

  • column annotation now flexible

• plotPCA

  • sample table accessible

• plotLoadings

  • made input accessible

• DEAnalysis

  • made input dds object accessible

• GSEA

  • made DEresults accessible
  • bugfix in canonical pathway enrichment

• added dotplotGSEA function

• uDEG

  • added functionality to plot uDEGs on Symbol level