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Integrated Differential Expression and Pathway analysis iDEP

Analyzes gene expression data from DNA microarray or RNA-Seq. iDEP integrates many commonly-used R/Bioconductor packages with comprehensive annotation databases. Normalized expression and RNA-Seq read counts are handled by two analysis workflows, and both involve a 4-stage process: pre-processing, Exploratory Data Analysis (EDA), differential expression, and pathway analysis and visualization. It can serve for preliminary analysis as it circumcises the need for many tedious tasks such as converting gene IDs and downloading software packages and annotations.

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iDEP forum

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iDEP classification

iDEP specifications

Interface:
Web user interface
Input format:
CSV, TXT
Version:
0.37
Maintained:
Yes
Restrictions to use:
None
Computer skills:
Basic
Stability:
Stable

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iDEP classification

iDEP specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Maintained:
Yes

iDEP distribution

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iDEP support

Maintainer

  • Steven Xijin Ge <>
  • Steven Xijin Ge <>

Additional information

https://idepsite.wordpress.com/

Credits

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Publications

Institution(s)

Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA

Funding source(s)

Partially supported by the National Science Foundation/EPSCoR Grant Number IIA-1355423 and by the State of South Dakota.

Link to literature

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