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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
NumPy Resource Report Resource Website 5000+ mentions |
NumPy (RRID:SCR_008633) | software resource | NumPy is the fundamental package needed for scientific computing with Python. It contains among other things: * a powerful N-dimensional array object * sophisticated (broadcasting) functions * tools for integrating C/C and Fortran code * useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. Sponsored by ENTHOUGHT | FASEB list |
is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is used by: Pingouin is related to: SciPy is related to: MNE software is related to: DE-Sim is required by: Wessim is required by: TomoMiner |
nif-0000-32013 | SCR_008633 | NumPy | 2026-08-01 12:03:34 | 6485 | |||||||||
|
Stimfit Resource Report Resource Website 10+ mentions |
Stimfit (RRID:SCR_016050) | data processing software, data analysis software, software application, software resource | Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. | electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis |
uses: NumPy uses: SciPy |
European Research Council ; Wellcome Trust ; Gatsby Charitable Foundation |
PMID:24600389 | Free, Available for download | SCR_016050 | 2026-08-01 12:05:26 | 38 | ||||||||
|
TomoMiner Resource Report Resource Website 1+ mentions |
TomoMiner (RRID:SCR_015045) | source code, software resource | Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging. | analysis platform, cryo electron subtomogram, subtomogram classification, subtomogram alignment, subtomogram averaging, subtomogram analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA requires: Python Programming Language requires: NumPy requires: SciPy requires: LAPACK linear algebra library requires: Cython C-Extensions for Python |
Available for download | biotools:tomominer | https://bio.tools/tomominer | SCR_015045 | 2026-08-01 12:12:33 | 3 | ||||||||
|
DE-Sim Resource Report Resource Website |
DE-Sim (RRID:SCR_018770) | software resource, software application, simulation software | Software object oriented discrete event simulation tool for complex, data driven modeling. Open source, Python based object oriented discrete event simulation tool that makes it easy to use large, heterogeneous datasets and high level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models. | Object oriented, discrete event simulation, data driven modeling, oriented discrete event simulation, computation model simulation |
is related to: NumPy is related to: SciPy is related to: Pandas is related to: SIMULA has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NSF 1649014; NIGMS R35 GM119771; Icahn Institute for Data Science and Genomic Technology |
Free, Available for download, Freely available | SCR_018770 | Discrete Event Simulation, object oriented Discrete Event-Simulation tool | 2026-08-01 12:06:04 | 0 | ||||||||
|
Elephant Resource Report Resource Website 10+ mentions |
Elephant (RRID:SCR_003833) | Elephant, ElePhAnT | software toolkit, data analysis software, software application, software resource, data processing software | The Electrophysiology Analysis Toolkit (Elephant) is a Python library that provides a modular framework for the analysis of experimental and simulated neuronal activity data, such as spike trains, local field potentials, and intracellular data. Elephant builds on the Neo data model to facilitate usability, to enable interoperability, and to support data from dozens of file formats and network simulation tools. Its analysis functions are continuously validated against reference implementations and reports in the literature. Visualizations of analysis results are made available via the Viziphant companion library. Elephant aims to act as a platform for sharing analysis methods across the field. | electrophysiology, analysis, spike train, local field potential, python |
uses: Neo uses: NumPy uses: SciPy is used by: NetworkUnit has parent organization: NeuralEnsemble |
PMID:31449837 | Free, Available for download, Freely available | nlx_158148 | https://github.com/NeuralEnsemble/elephant | SCR_003833 | Elephant - Electrophysiology Analysis Toolkit, Electrophysiology Analysis Toolkit | 2026-08-01 12:02:26 | 29 | |||||
|
MNE software Resource Report Resource Website 50+ mentions |
MNE software (RRID:SCR_005972) | MNE | data visualization software, software toolkit, data analysis software, software application, software resource, data processing software | Software suite for processing magnetoencephalography and electroencephalography data. Open source Python software for exploring, visualizing, and analyzing human neurophysiological data including MEG, EEG, sEEG, ECoG . Implements all functionality of MNE Matlab tools in Python and extends capabilities of MNE Matlab tools to, e.g., frequency-domain and time-frequency analyses and non-parametric statistics. | Magnetoencephalography data processing, electroencephaography data processing, data analysis, eeg, meg, linux, mac osx, human neurophysiological data, statistics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: MNE-BIDS is related to: MATLAB is related to: NumPy is related to: SciPy is related to: Matplotlib is related to: Mayavi: 3D Scientific Data Visualization and Plotting Software Project is related to: NiBabel |
NIBIB R01 EB009048; NIBIB P41 EB015896; NCRR P41 RR014075; NIDCD F32DC012456; NSF 0958669; NSF 1042134; European Research Council (ERC) StG-263584 |
PMID:24161808 PMID:24431986 |
Free, Available for download, Freely available | nlx_151346 | https://sources.debian.org/src/python3-mne/, http://www.nitrc.org/projects/mne, http://www.nmr.mgh.harvard.edu/martinos/ncrr/sofMNE.html, https://github.com/mne-tools/, https://mne.tools/ | SCR_005972 | Minimum Norm Current Estimates Software, Minimum Norm Current Estimates, MNE tools for MEG and EEG data analysis, MNE-Python | 2026-08-01 12:03:02 | 97 | ||||
|
Wessim Resource Report Resource Website 1+ mentions |
Wessim (RRID:SCR_002567) | data analysis software, software application, software resource, sequence analysis software, data processing software, simulation software | Software simulator for a targeted resequencing generally known as exome sequencing. Wessim generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation. | resequencing simulator, artificial dna fragments, exome sequencing, next generation sequencing, ngs, python |
uses: Python Programming Language is listed by: OMICtools requires: SAMTOOLS requires: NumPy requires: GemSIM |
PMID:23413434 | Free, Available for download, Freely available | OMICS_00259 | SCR_002567 | 2026-08-01 12:07:32 | 3 | ||||||||
|
SciPy Resource Report Resource Website 10000+ mentions |
SciPy (RRID:SCR_008058) | software resource, software application | A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console. | python, software, open source |
uses: Python Programming Language is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is listed by: SoftCite is related to: IPython is related to: NumPy is related to: IPython Notebook is related to: MNE software is related to: DE-Sim is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens |
Public, Free | nif-0000-10422 | SCR_008058 | SciPy, Scientific Tools for Python | 2026-08-01 12:10:51 | 12935 | ||||||||
|
Sklearn Resource Report Resource Website 100+ mentions |
Sklearn (RRID:SCR_019053) | software resource, software toolkit | Software Python package part of nonnegative matrix factorization NMF. Features various classification, regression and clustering algorithms including support vector machines, random forests, gradient boosting, k-means and DBSCAN, and is designed to interoperate with Python numerical and scientific libraries NumPy and SciPy. | Non negative matrix factorization, machine learning library, Python programming language |
uses: SciPy uses: NumPy is used by: peakachu |
Free, Available for download, Freely Available | https://github.com/scikit-learn/scikit-learn, https://scikit-learn.org/stable/ | SCR_019053 | Scikit-learn, scikits.learn | 2026-08-01 12:11:11 | 257 | ||||||||
|
Pingouin Resource Report Resource Website 50+ mentions |
Pingouin (RRID:SCR_022261) | software resource, software toolkit | Open source statistical package written in Python 3 and based mostly on Pandas and NumPy. Designed for users who want simple yet exhaustive stats functions. | statistical functions, Python 3 | uses: NumPy | DOI:10.21105/joss.01026 | Free, Available for download, Freely available | https://github.com/raphaelvallat/pingouin | SCR_022261 | 2026-08-01 12:11:07 | 57 | ||||||||
|
PyDSTool Resource Report Resource Website 10+ mentions |
PyDSTool (RRID:SCR_014771) | software resource, software application, standalone software, simulation software | Integrated simulation and analysis environment for dynamic systems models of physical systems. It supports symbolic math, optimization, phase plane analysis, continuation and bifurcation analysis, data analysis, and other tools for modeling. It is written in Python with some underlying C and Fortran legacy code. | integrated software, integrated analysis, model, simulation software, physical system, python |
uses: NumPy uses: SciPy |
DOI:10.1371/journal.pcbi.1002628 | Open source, Available for download, Acknowledgement requested | SCR_014771 | 2026-08-01 12:08:45 | 17 |
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