IDEP

iDEP (integrated Differential Expression and Pathway analysis) is a web-based tool for analyzing RNA-seq data, available at http://ge-lab.org/idep/. It reads in gene-level expression data (read counts or FPKM), performs exploratory data analysis (EDA), differential expression, pathway analysis, biclustering, and co-expression network analysis. iDEP also accepts DNA microarray data or other gene-level expression data, such as those from Chip-seq or proteomics studies... iDEP is a user-friendly Shiny app powered by many widely-used R/Bioconductor packages for analyzing gene expression data. For EDA, it performs hierarchical clustering, k-means clustering, and principal component analysis (PCA). iDEP detects differentially expressed genes using the limma and DESeq2 packages. For a group of co-expressed genes, it identifies enriched gene ontology (GO) terms as well as transcription factor binding motifs in promoter sequences. Pathway analysis can be performed using GSEA(Gene Set..