Numpy protocols

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Numpy specifications

Information


Unique identifier OMICS_20143
Name Numpy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.13.1
Stability Stable
Maintained Yes

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Tuto: https://docs.scipy.org/doc/numpy-dev/user/quickstart.html

Numpy in pipelines

 (2)
2017
PMCID: 5460138
PMID: 28603644
DOI: 10.1038/s41540-017-0003-6

[…] as control, except when noted. we used binomial tests to compare to a given percentage. if it is not mentioned otherwise, the compared ratio is first neighbour proteins to all proteins. we used the numpy and scipy packages for python for statistical analysis. , for creating the network figures, version 3.1 of cytoscape was used. violin plots have been made with the vioplot r package, […]

2016
PMCID: 5098983
PMID: 27853558
DOI: 10.1098/rsos.160451

[…] the attractive landmarks. these time sequences were calculated according to the number of fish present near the landmarks. all scripts were coded in python using scientific and statistic libraries (numpy, pylab, scilab and matplotlib)., to compute the number of majority events, the number of fish was averaged over the 15 frames of every second. this operation guarantees that a majority event […]


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Numpy in publications

 (601)
PMCID: 5935699
PMID: 29728622
DOI: 10.1038/s41467-018-04241-5

[…] ps://github.com/christophmark/bayesloop). the website bayesloop.com further provides access to code examples, tutorials and documentation. bayesloop uses functionality of other python modules, namely numpy, scipy (http://www.scipy.org), sympy, matplotlib, pathos, and tqdm., the coal-mining accident data shown in fig.  are provided as supplementary data . the cancer cell trajectories shown in fig.  […]

PMCID: 5931971
PMID: 29720620
DOI: 10.1038/s41467-018-04104-z

[…] to each sample’s dose–response curve and integrating the fitted equation over the region corresponding to the second response curve. these equations were fit to the data using the polyfit module in numpy, a fundamental package for scientific computing using python. we chose to use a six-dimensional least-square polynomial equation because it captures the dynamics of the second response curve […]

PMCID: 5938415
PMID: 29765309
DOI: 10.3389/fnsys.2018.00007

[…] roi. the pseudocode in figure illustrates the complete process. the program was written in python using opencv3 (open source computer vision library; opencv.org), pyqt5, scikit-learn, scipy, and numpy; and is available for download at http://www.github.com/developerjose/vision-rat-brain., to test the computer vision algorithm, three experiments were conducted. experiment 1a, […]

PMCID: 5946844
PMID: 29432771
DOI: 10.1016/j.ijpara.2017.11.003

[…] for normalisation, a subsampled otu table was generated by random sampling (without replacement) of the input otu table using an implementation of the mersenne twister algorithm (http://www.numpy.org). cumulative-sum scaling (css) and log2 transformation were applied to account for the non-normal distribution of taxonomic counts data. statistical analyses were conducted on the calypso […]

PMCID: 5960325
PMID: 29712863
DOI: 10.1073/pnas.1801895115

[…] rate up to 1 fps) and movies (1920×1080 pixels at 24 fps) are taken with a nikon d7000., all image analyses were done with custom-developed python scripts, based on usual scientific libraries (numpy 1.11.1 and matplotlib 1.5.1) and image processing tools from scikit-image (version 0.12.3) and opencv (version 2.4.11)., statolith pile angles were measured using the following method. first, […]


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