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pixelator: Citations

Pipeline tools

  • pixelator

    Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.

  • cutadapt

    Martin, Marcel. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.Journal 17, no. 1 (May 2, 2011): 10–12. https://doi.org/10.14806/ej.17.1.200.

  • fastp

    Chen, Shifu. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” IMeta 2, no. 2 (2023): e107. https://doi.org/10.1002/imt2.107.

  • networkx

    Aric A. Hagberg, Daniel A. Schult and Pieter J. Swart, “Exploring network structure, dynamics, and function using NetworkX”, in Proceedings of the 7th Python in Science Conference (SciPy2008), Gäel Varoquaux, Travis Vaught, and Jarrod Millman (Eds), (Pasadena, CA USA), pp. 11–15, Aug 2008

  • graspologic

    Chung, J., Pedigo, B. D., Bridgeford, E. W., Varjavand, B. K., Helm, H. S., & Vogelstein, J. T. (2019). GraSPy: Graph Statistics in Python. Journal of Machine Learning Research, 20(158), 1-7.

  • local G

    Bivand, R.S., Wong, D.W.S. Comparing implementations of global and local indicators of spatial association. TEST 27, 716–748 (2018). https://doi.org/10.1007/s11749-018-0599-x

  • dsb

    Mulè, M.P., Martins, A.J. & Tsang, J.S. Normalizing and denoising protein expression data from droplet-based single cell profiling. Nat Commun 13, 2099 (2022). https://doi.org/10.1038/s41467-022-29356-8