Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.
Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Department of Pharmacy, Saarland University, Campus E8 1, 66123 Saarbrücken, Germany.
Nucleic Acids Res. 2021 Jul 2;49(W1):W397-W408. doi: 10.1093/nar/gkab268.
Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.
分析小非编码 RNA 测序数据的所有特征可能既要求高又具有挑战性。为了方便这一过程，我们开发了 miRMaster。在对超过 125000 个人类样本和超过 4 年的 1.5 万亿个人类小 RNA 读数进行分析后，我们推出了 miRMaster 2，它具有广泛的更新和新功能。我们扩展了参考数据集，因此 miRMaster 2 现在支持 8 个物种（例如人类、小鼠、鸡、狗、牛）和 10 个非编码 RNA 类（例如 microRNAs、piRNAs、tRNAs、rRNAs、circRNAs）的分析。我们还整合了新的下游分析模块，如使用 UMAP 的批次效应分析或样本嵌入，以及更新默认包含的注释数据库（miRBase、Ensembl、GtRNAdb）。为了适应单细胞小 RNA 测序数据日益普及的趋势，我们整合了一个用于独特分子标识符（UMI）处理的模块。此外，根据用户反馈改进了输出表和图形，现在支持新出现的社区输出格式（例如 miRGFF3）。最后，我们将差异表达分析与 miRNA 富集分析工具 miEAA 集成在一起。miRMaster 可在 https://www.ccb.uni-saarland.de/mirmaster2 上免费获得。
Nucleic Acids Res. 2021-7-2
Nucleic Acids Res. 2020-7-2
Nucleic Acids Res. 2020-7-2
Nucleic Acids Res. 2023-7-5
Nucleic Acids Res. 2017-9-6
Bioinformatics. 2013-12-3
PLoS One. 2020-5-28
Nucleic Acids Res. 2012-6-16
Nucleic Acids Res. 2016-7-8
Bioinformatics. 2020-2-1
Brief Bioinform. 2021-7-20
Nucleic Acids Res. 2021-1-25
Proc Natl Acad Sci U S A. 2020-12-22
Biomolecules. 2020-11-20
Nucleic Acids Res. 2021-1-8
Proc Natl Acad Sci U S A. 2020-9-25
Nucleic Acids Res. 2020-7-2
Nucleic Acids Res. 2020-7-2
Genomics Proteomics Bioinformatics. 2019-12-4
Zotero 插件
