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What is special about GCEN?

GCEN aims to make it easier for biologists to construct gene co-expression networks and predict gene function. It has three notable features: easy-to-use, high-speed and low-memory-usage, and cross-platform. GCEN can carry out gene co-expression network analysis on a personal computer for tens of thousands of genes in RNA-Seq research.

Command-line scares you off?

Actually, GCEN is really easy to use! All you need is to download it. There are no dependencies or sophisticated programming skills required. The software package includes a README file and sample data that demonstrate how to use it effectively.

How to start building a gene co-expression network?

Only gene expression profiles are required. We provide two programs generate_expr_matrix_from_rsem and generate_expr_matrix_from_stringtie to obtain the gene expression profiles from outputs of RSEM and StringTie.

GCEN does not support CSV files?

Yes. Most input and output files of GCEN are tab-separated values (TSV) files. We provide two programs csv_to_tsv and tsv_to_csv for converting TSV and CSV files to each other.

What is required to use gene co-expression networks to predict gene function?

In addition to the gene co-expression network obtained in the previous step, some known gene function annotations are also needed. GO annotations for most model organisms can be downloaded from the Gene Ontology Consortium. KEGG annotations of protein-coding protein genes can be obtained by KAAS. InterProScan is a tool to automatically annotate proteins, which can also obtain GO and KEGG of proteins.

What should you do if you can't solve a problem?

Connecting with our users is really important to us. Whether you have a question or a suggestion, we'd love to hear from you! You can contact us by E-mail, WeChat, or Telegram.