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scpdata: a data package for single-cell proteomics

Authors :
Vanderaa, Christophe
Gatto, Laurent
Gatto, Laurent
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."]}

Details

Language :
English
Database :
OpenAIRE
Accession number :
edsair.doi.dedup.....81c837fdf03fa8fac2b7aa05b8fd523d
Full Text :
https://doi.org/10.5281/zenodo.3566018