FindIT2

FindIT2 (Find Influential TFs and Targets) is a R/Bioconductor package designed to address the need for a comprehensive data processing and analysis framework for inferring influential transcription factors (TFs) based on ChIP-seq/ATAC-seq datasets. Transcription factors play crucial roles in gene expression regulation. With the increasing use of high-throughput sequencing methods, a growing demand exists for tools that can annotate and process multi-omics data effectively.
FindIT2 supports a complete framework for annotating ChIP-seq/ATAC-seq peaks, identifying TF targets by integrating ChIP-seq and RNA-seq datasets and inferring influential TFs based on different types of data input.

Topic

ChIP-seq;RNA-Seq;Transcription factors and regulatory sites;Gene regulation;Chromosome conformation capture

Detail

  • Operation: Peak calling;Differential gene expression profiling;Peak detection

  • Software interface: Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.9.0

  • Credit: National Natural Science Foundation of China, Strategic Priority Research Program of the Chinese Academy of Sciences.

  • Input: -

  • Output: -

  • Contact: Guandong Shang shangguandong1996@163.com

  • Collection: -

  • Maturity: Stable

Publications

  • FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.
  • Shang GD, et al. FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data. FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data. 2022; 23:272. doi: 10.1186/s12864-022-08506-8
  • https://doi.org/10.1186/S12864-022-08506-8
  • PMID: 35392802
  • PMC: PMC8988339

Download and documentation

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