Software for data-analysis
Upstream packages
The following tools are among the software currently tested in NeuroFedora and can be installed directly from upstream forges (e.g. PyPi). You can see the tests results here.
Python packages
| Software | Summary | pip (PyPi) | Notes |
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Electrophys Feature Extract Library (eFEL). |
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Elephant is a package for analysis of electrophysiology data in Python. |
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Utilities to read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files. |
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Python SDK for interacting with neuroscience data via the Boss API. |
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Spike detection and automatic clustering for spike sorting. |
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Unmaintained upstream |
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A minimalistic framework for numerical association rule mining. |
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Pingouin: statistical package for Python. |
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Python package to handle probe layout, geometry and wiring to device. |
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Python library for reading files in Axon Binary Format (ABF). |
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pybv - a lightweight I/O utility for the BrainVision data format. |
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22 CAnonical Time-series Features. |
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A Python library for analysis of electrophysiological data. |
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Machine learning for multivariate data with Riemannian geometry. |
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Unified complex network and recurrence analysis toolbox. |
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Python library for importing XDF (Extensible Data Format). |
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System packages
The following are included in the repositories:
| Software | Install with | Notes |
|---|---|---|
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A Python package for AMPL/GMPL datafile parsing. |
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Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns. |
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A fully automated high-quality brain tetrahedral mesh generation toolbox. |
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Python implementations of contextual bandits algorithms. |
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Cython interface for the interior point optimzer IPOPT. |
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A fast implementation of the edit distance (Levenshtein distance) in Python. |
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Application designed to track multiple objects in video recording. |
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File identification library for Python. |
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A medical-image based 3-D mesh generation and analysis toolkit. |
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A 3-D Monte Carlo photon transport simulation toolbox. |
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Python package for multi-electrode array (MEA) handling and stimulation. |
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A 3-D mesh-based Monte Carlo photon transport simulator. |
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Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis. |
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A library for the computation of Nash equilibria in two player games. |
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A Python package to analyze and simulate neural time series, using digital signal processing. |
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Large-scale synthesis of functional neuroimaging data. |
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AutoML in Python. |
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Framework for solving classification tasks using nature-inspired algorithms. |
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A Python package for solving optimization problems. |
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Timeseries analysis for neuroscience data. |
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File-format to store metadata in an organized way. |
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A C++ package for solving the forward problems of electroencephalography (EEG) and magnetoencephalography (MEG). |
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A Python package for working with NWB files. |
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A Python library for the numerical analysis of spiketrain similarity |
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PySwarms is an extensible research toolkit for particle swarm optimization (PSO) in Python. |
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Sensitivity Analysis Library. |
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GUI for generating hybrid ground-truth spiking data |
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Utils for streaming large files (S3, HDFS, gzip, bz2, and more). |
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A fast and scalable solution for spike sorting of large-scale extracellular recordings. |
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Import, export, process, analyze and view triangular meshes. |
Software that is in the queue for inclusion is listed here.
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