Computational Systems Biology Methods and Protocols.7z

1.3 iSeq: A
Web-Based Server for
RNA-seq Data Analysis
and Visualization

In this article, we introduce iSeq, a Web-based analysis suite spe-

cially designed for RNA-seq data analysis, which integrates robust

analysis methods, data visualization schemes, and functional analy-

sis tools to analyze and visualize RNA-seq data (Fig.1). Users can

explore their data through an intuitive graphical interface and focus

on deciphering expressional patterns and functional relevance cen-

tral to their experimental questions, without having to master

complex computational and programming skills.

A comparison between iSeq and other Web-based RNA-seq

analysis tools is summarized in Table1. The greatest distinction

of iSeq lies in that it focuses on a complete analytical workflow

Normalization

PreprocessCore

DESeq

Quality Check

affy

Uploading

Heat Map

RColorBrewer

gplots

Enrichment

goseq

RDAVIDWebService

org.Hs.eg.db

org.Mm.eg.db

DEG Calling

DESeq

Bar Plot

ggplot

PCA Analysis

ggfortify

Fig. 1An overview of iSeq analysis workflow

Table 1
Comparison between iSeq and other Web-based RNA-seq analysis tools

iSeq Galaxy Seven Bridges START RAP CANEapp
Local installation Yes Yes No Yes No No
Skill requirements Low High High Low Middle Middle
Mapping No Yes Yes No Yes Yes
RNA editing No Yes Yes No Yes No
Quality checka Yes No No No No No
Normalization Yes Yes Yes No Yes Yes
DEG calling Yes Yes Yes No Yes Yes
Visualization Rich Basic Basic Rich Basic No
aQuality check here refers to checking the comparability among samples which is susceptible to batch effects. Not to be
confused with checking read quality as is often done by FastQC and similar tools

170 Chao Zhang et al.