scEpiTools is a user-friendly database to interrogate analytic tools for single-cell epigenomic data. Single-cell epigenomics methodologies, including DNA methylation, chromatin accessibility, histone modifications, chromosome conformation are becoming a powerful tool in studies of cellular plasticity and diversity (Schwartzman, O., Tanay, A, Nature Reviews Genetics, 2015). For better interrogating single-cell epigenomic tools and enable researchers to find suitable analytical tools for different needs, we have collected over 700 single-cell epigenetic tools and developed this database, scEpiTools.

scEpiTools has five main application scenarios:

1. Searching of epigenomic tools, also with reviews, sequencing technologies, and studies.
2. Browsing of various epigenomic tools categoried into 14 main task categories and 104 subcategories and detailed annotations, such as the tool methodology, baseline methods and dependency. Various statistical measures such as the number distribution of tools across various platforms, journals, methodologies and licenses are provided.
3. Personalized recommendation
   • Researchers can conduct comprehensive evaluation and comparison on epigenomic tools with the help of scEpiTools when developing algorithms.
   • Researchers can conveniently find relevant review articles when navigating the vast sea of available tools via recommend score of reviews provided on scEpiTools.
   • Biologists can find the tools for sequencing technology conveniently and intuitively with the help of recommend score of sequencing technology provided on scEpiTools.
   • Researchers are able to find suitable studies conveniently via three novel recommendation scores, facilitating the analysis and benchmarking.
4. Users without experience in coding can undertake single-cell epigenomic data analysis via intuitive tutorial-style interfaces.
5. Researcher who is unfamiliar with the environment configuration or who repeatedly has difficulty installing the environment can download the tool environment from scEpiTools from the Download page.

User-friendly searching and recommendation

Search

• Advanced searching with multiple filters
• Personalized recommendation

Hierarchical categorization and browsing

Browse

• Tree based hierarchical categorization
• Various statistics measures

Comprehensive analysis and detailed tutorial

Analysis

• Build-in kernel online analysis
• Detailed tutorial of the analysis pipeline

scMCs: a framework for single cell multi-omics data integration and multiple clusterings. Ren, L., Wang, J., Li, Z., Li, Q., & Yu, G. Bioinformatics. 2023;39(4):btad133

Single-cell biological network inference using a heterogeneous graph transformer. Ma, A., Wang, X., Li, J., et al. Nature Communications. 2023;14(1), 964

Decision level integration of unimodal and multimodal single cell data with scTriangulate. Li, G., Song, B., Singh, H., et al. Nature communications. 2023;14(1), 406.

scChIX-seq infers dynamic relationships between histone modifications in single cells. Yeung, J., Florescu, M., Zeller, P., et al. Nature Biotechnology. 2023

A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. Wang, Y., Lian, B., Zhang, H., et al. Bioinformatics. 2023;39(1):btad005

• Number of tools within scEpiTools has been updated to 766.

  9 Apr 2024
• Number of tools within scEpiTools has been updated to 729.

  9 Feb 2024
• Number of tools within scEpiTools has been updated to 678.

  9 Dec 2023
• Number of tools within scEpiTools has been updated to 643.

  9 Oct 2023
• Number of tools within scEpiTools has been updated to 622.

  16 Aug 2023
• We proposed a novel ensemble kernel, named scEpiEnsemble, for more accurate analysis of single-cell epigenomic data.

  3 Apr 2023
• Signac and SnapATAC kernels have been added to the Analysis Page.

  24 Mar 2023
• Number of tools within scEpiTools has been updated to 553.

  03 Mar 2023
• Provided a demo for the analysis of single-cell epigenomics data.

  15 Dec 2022
• Detailed statistic measures have been added to the Browse page.

  1 Dec 2022
• 334 tools have been added to scEpiTools.

  25 Nov 2022
• Version 1.0 of scEpiTools has been released.

  20 Oct 2022