Table of Contents
Supported Analysis:
• Over-representation analysis
• Gene set enrichment analysis
• Enriched subnetwork analysis
• Time series analysis
Supported data types:
• Gene list
• Named phenotypes preprocessed from either RNA-seq, micro-array, RNAi or CRISPR
• ‘Time Series’ data
Supported ontologies/pathways:
Gene Ontology: GO
• Molecular function (MF)
• Biological process (BP)
• Cellular component (CC)
Kyoto Encyclopedia of Genes and Genomes pathways: KEGG
Molecular Signatures Database: MSigDB v6.1
• h: hallmark gene sets
• c1: positional gene sets
• c2: curated gene sets
• c3: motif gene sets
• c4: computational gene sets
• c5: GO gene sets
• c6: oncogenic signatures
• c7: immunologic signatures
Customized gene sets
Supported species:
• Gene Ontology and KEGG gene sets support any species that have an OrgDb object in
Bioconductor.
• MSigDB gene sets only support all 8 gene set collections for Homo Sapiens and three
gene set collections: ‘c2’, ‘c6’ and ‘c7’ for Mus musculus.
Visualization:
• GSEA plot
• Enrichment map
• Enriched subnetwork
• Interactive report for all results
Before starting the demonstration, you need to install and load the following packages:
library(HTSanalyzeR2)
library(org.Hs.eg.db)
library(KEGGREST)
library(GO.db)
library(igraph)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)