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scpdata: a data package for single-cell proteomics
- Publication Year :
- 2019
- Publisher :
- Zenodo, 2019.
-
Abstract
- Recent advances in sample preparation, processing and mass spectrometry (MS) have allowed the emergence of MS-based single-cell proteomics (SCP). However, bioinformatics tools to process and analyze these new types of data are still missing. In order to boost the development and the benchmarking of SCP methodologies, we are developing the scpdata experiment package. The package will distribute published and curated SCP data sets in standardized Bioconductor format.<br />{"references":["Y. Zhu, P. D. Piehowski, R. Zhao, J. Chen, Y. Shen, R. J. Moore, A. K. Shukla, V. A. Petyuk, M. Campbell- Thompson, C. E. Mathews, R. D. Smith, W.-J. Qian, and R. T. Kelly, \"Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells,\" Nat. Commun., vol. 9, p. 882, Feb. 2018.","B. Budnik, E. Levy, G. Harmange, and N. Slavov, \"SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation,\" Genome Biol., vol. 19, p. 161, Oct. 2018.","H. Specht, E. Emmott, T. Koller, and N. Slavov, \"High-throughput single-cell proteomics quantifies the emer- gence of macrophage heterogeneity.\" June 2019.","G. Huffman, H. Specht, A. T. Chen, and N. Slavov, \"DO-MS: Data-Driven optimization of mass spectrometry methods.\" Jan. 2019.","L. Gatto and K. S. Lilley, \"MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation,\" Bioinformatics, vol. 28, pp. 288–289, Jan. 2012."]}
- Subjects :
- proteomics
Bioconductor
mass spectrometry
single cell
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....81c837fdf03fa8fac2b7aa05b8fd523d
- Full Text :
- https://doi.org/10.5281/zenodo.3566018