Published October 12, 2022
| Version 6
Software
Open
NanoString Differential Expression Analysis with NanoStringDiff package
Description
Script for Nanostring analysis based on NanoStringDiff package (NanoStringAnalysis_NanoStringDiff_v5_general.R) allowing for multi-group analysis and for plotting results along with gene enrichment analysis (NanoStringAnalysis_eval_graph_GSEA_general_v6.R). Non-script files are example data for showing inputs and outputs.
Files
DE_bubble_multi.tiff
Files
(1.3 MB)
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Additional details
References
- wang h, zhai t, wang c (2022). NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data. R package version 1.26.0.
- Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu x, Liu S, Bo X, Yu G (2021). "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data." The Innovation, 2(3), 100141. doi: 10.1016/j.xinn.2021.100141.
- Blighe K, Rana S, Lewis M (2022). EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling. R package version 1.14.0, https://github.com/kevinblighe/EnhancedVolcano.
- Ashburner, M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25, 25-29 (2000).
- The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res 49, D325-d334 (2021).
- Yu, G., et al. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26, 976-978 (2010).
- Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30 (2000).
- Fabregat, A., et al. The Reactome pathway Knowledgebase. Nucleic Acids Res 44, D481-487 (2016).
- Yu, G. & He, Q.-Y. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 12, 477-479 (2016).
- Subramanian, A., et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences 102, 15545 (2005).
- Dolgalev, I. msigdbr: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format. R package version 7.2.1. (2020).
- W., L. gageData: Auxillary data for gage package. R package version 2.28.0. (2020).