Cell Nucleic seQuencing Single Acid Ribo
The full pipeline lives in consecutivizer.ipynb.
Libraries used -
SCANPY: large-scale single-cell gene expression data analysis
F. Alexander Wolf, Philipp Angerer, Fabian J. Theis
Genome Biology 2018 Feb 06. doi: 10.1186/s13059-017-1382-0.
Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland, Tyler Reddy, David Cournapeau, Evgeni Burovski, Pearu Peterson, Warren Weckesser, Jonathan Bright, Stéfan J. van der Walt, Matthew Brett, Joshua Wilson, K. Jarrod Millman, Nikolay Mayorov, Andrew R. J. Nelson, Eric Jones, Robert Kern, Eric Larson, CJ Carey, İlhan Polat, Yu Feng, Eric W. Moore, Jake VanderPlas, Denis Laxalde, Josef Perktold, Robert Cimrman, Ian Henriksen, E.A. Quintero, Charles R Harris, Anne M. Archibald, Antônio H. Ribeiro, Fabian Pedregosa, Paul van Mulbregt, and SciPy 1.0 Contributors. (2020) SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nature Methods, 17(3), 261-272. DOI: 10.1038/s41592-019-0686-2.
Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020). DOI: 10.1038/s41586-020-2649-2. (Publisher link).
anndata: Annotated data
Isaac Virshup, Sergei Rybakov, Fabian J. Theis, Philipp Angerer, F. Alexander Wolf
JOSS 2024 Sep 16. doi: 10.21105/joss.04371.
Siu Kwan Lam, Antoine Pitrou, and Stanley Seibert. 2015. Numba: a LLVM-based Python JIT compiler. In Proceedings of the Second Workshop on the LLVM Compiler Infrastructure in HPC (LLVM '15). Association for Computing Machinery, New York, NY, USA, Article 7, 1–6. https://doi.org/10.1145/2833157.2833162