CAGEr

CAGEr is an R package to enhance Cap Analysis of Gene Expression (CAGE) data, which are crucial for analyzing transcription start sites (TSS) at a high resolution. Despite the detailed insights CAGE data provide into promoter dynamics and TSS usage, their potential has been underutilized due to the lack of efficient tools for data handling and integration with other genomic information. Addressing this gap, CAGEr offers a comprehensive suite of novel methods for the differential analysis of TSS usage and promoter dynamics, along with functionalities for processing CAGE data and mining promoteromes.

It significantly facilitates access to a vast array of TSS data, including a rich collection from published CAGE datasets and the extensive FANTOM5 TSS resource for various human and mouse cells and tissues. This tool simplifies the integration of precise, context-specific TSS data into broader genomic analyses.

Topic

Gene expression;Transcription factors and regulatory sites;Sequencing

Detail

  • Operation: Transcriptional regulatory element prediction

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 2.8.0

  • Credit: The Norwegian Research Council (YFF), Bergen Research Foundation (BFS), European Union (EU) FP6 integrated project EuTRACC, FP7 integrated project ZF Health, Medical Research Council UK, Ministry of Education, Culture, Sports, Science and Technology in Japan to RIKEN Center for Life Science Technologies, RIKEN Preventive Medicine and Diagnosis Innovation Program.

  • Input: -

  • Output: -

  • Contact: Charles Plessy charles.plessy@oist.jp

  • Collection: -

  • Maturity: Stable

Publications

  • CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.
  • Haberle V, et al. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses. 2015; 43:e51. doi: 10.1093/nar/gkv054
  • https://doi.org/10.1093/nar/gkv054
  • PMID: 25653163
  • PMC: PMC4417143
  • CAGER: classification analysis of gene expression regulation using multiple information sources.
  • Ruan J and Zhang W. CAGER: classification analysis of gene expression regulation using multiple information sources. CAGER: classification analysis of gene expression regulation using multiple information sources. 2005; 6:114. doi: 10.1186/1471-2105-6-114
  • https://doi.org/10.1186/1471-2105-6-114
  • PMID: 15890068
  • PMC: PMC1174863

Download and documentation

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