“…GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. …”
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“…Here we introduce the iPRD software ReaDDy 2, which provides a Python interface in which the simulation environment, particle interactions and reaction rules can be conveniently defined and the simulation can be run, stored and analyzed. …”
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“…CLEESE works by cutting recordings in small successive time segments (e.g. every successive 100 milliseconds in a spoken utterance), and applying a random parametric transformation of each segment’s pitch, duration or amplitude, using a new Python-language implementation of the phase-vocoder digital audio technique. …”
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“…AVAILABILITY AND IMPLEMENTATION: Software packages (available in Python, R, Matlab and Java) are freely available at https://github.com/cmap. …”
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“…Here, we introduce EMUlator a Python-based isotope simulator which is developed on Elementary Metabolite Unit (EMU) algorithm, an efficient and powerful algorithm for isotope modeling. …”
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“…The core program (tree-traversing approach) of cano-eMLST is implemented in Perl and Python. All the necessary dependencies and environmental settings are provided in the encapsulated version (VirtualBox or VMware) and self-installation version (all use source code and libraries).…”
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“…Results on simulated and real datasets demonstrate that ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using a parametric mapping function, and scales linearly to hundreds of thousands of cells. ivis is made publicly available through Python and R interfaces on https://github.com/beringresearch/ivis.…”
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“…Files necessary for adding to and amending the dataset are also included, plus a python class containing useful methods for interacting with the dataset, and IC classifications produced by several existing IC classifiers. …”
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“…This server provides a user-friendly interface for exploring longitudinal behavioral data taking advantage of the Pergola Python library. Using the server, users can process the data applying some basic operations, such as binning or grouping, while formatting the data into existing genomic formats. …”
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“…Inside of the Raspberry Pi, a Python script detects the openings of the doors, and classifies the events between attempts of finding something without success and the events of actually finding it, in order to measure the user’s memory concerning the objects’ locations (among the three compartments of the smart cupboard). …”
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“…To facilitate wider use of such techniques within neuroimaging and general neuroscience communities, our work provides several tools for visualizing, interacting with, and grounding TDA-generated graphical representations in neurophysiology. Through Python-based Jupyter notebooks and open datasets, we provide a platform to assess and visualize different intermittent stages of Mapper and examine the influence of Mapper parameters on the generated representations. …”
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“…AVAILABILITY AND IMPLEMENTATION: HeteroGenesis and w-Wessim are freely available under the GNU General Public Licence from https://github.com/GeorgetteTanner, implemented in Python and supported on linux and MS Windows. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.…”
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“…SAMDUDE is written in Python and is freely available at https://github.com/ihwang/SAMDUDE.…”
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“…CONCLUSIONS: The new method for the differential expression analysis of proteomic data is available as an easy to use Python package.…”
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“…AVAILABILITY AND IMPLEMENTATION: svtools is implemented in Python and freely available (MIT) from https://github.com/hall-lab/svtools. …”
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“…For the first time, mPies facilitates the automatization of reliable taxonomic and functional consensus annotations at the protein group level, minimizing the well-known protein inference issue, which is commonly encountered in metaproteomics. mPies’ workflow is highly customizable with regards to input data, workflow steps, and parameter adjustment. mPies is implemented in Python 3/Snakemake and freely available on GitHub: https://github.com/johanneswerner/mPies/. …”
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“…We significantly reduced this time by developing a software kit, written in Python, to evaluate instrument and sample QC, along with data usability. …”
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“…We describe an automated method of sizing droplets as they are produced using video recording and custom Python code. The sustainable generation of such size-controlled PUMCs, potential replacements for commercial encapsulated systems, will allow new insights into the effect of particle size on performance.…”
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“…Finally, we introduce the Python library NetComp that implements the graph distances used in this work.…”
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“…A webtool was developed to browse these results for genes or tissues of interest. An example python implementation of SPECS is available at https://github.com/celineeveraert/SPECS. …”
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