From Fedora Project Wiki
Suggest more software!
Please use this form to suggest more software for inclusion in NeuroFedora.

There is a good amount of overlap with other SIGs and Spins and some categories of NeuroFedora can be seen as BigData, Fedora-Medical, ML, Octave and SciTech in general.

Please add software that needs to be packaged to the appropriate table with the status "needs packaging". If a package is in a COPR repository, a status of "COPR" can be used. Once a package is in review, the status should be "In review", and of course, once a package is in the repositories, the final status would be "Packaged".

Please feel free to reorganise the tables as required.

If you use a package that is not available in Fedora yet, please feel free to e-mail us and we'll look into providing it. You can either contact us on the mailing list, the IRC channel, or e-mail us privately too!

Packages for Distributed Computing

Package Summary Status Comment
example Packaged
h5py A python interface to the HDF5 library Packaged
mpi4py Python bindings for MPI---MPICH and OpenMPI Packaged

Packages for Image analysis

Package Summary Status Comment
ctk The CTK core library for Image analysis Packaged
dcm2niix Conver neuroimaging data from NIFTI format to DICOM Packaged
isis Framework to access a large variety of image libraries Needs import
libminc Library to work with the MINC file format Packaged
python-nibabel Python package to access a cacophony of neuro-imaging file formats Packaged
python-pydicom Read, modify, and write DICOM files with Python Packaged
rubygem-nifti Pure-ruby library for handling NIfTI data in Ruby Packaged
python-nilearn Python module for fast and easy statistical learning on NeuroImaging data Needs packaging. Dead review here: 1291877
isis Framework to access a large variety of image processing libraries Reviewed: needs import 1279176
itktools Practical command line tools based on the ITK Reviewed: needs import 1279579
DiffusionKurtosisFit Code to reconstruct the Diffusion Kurtosis Tensor from Diffusion Weighted MRI Packaged
petpvc Tools for partial volume correction (PVC) in positron emission tomography (PET) Packaged
python-commit Convex Optimization Modeling for Microstructure Informed Tractography Needs review. Dead review here: 1288759
python-petlink Decode and encode PETlink streams Needs packaging. Dead review here 1288836
python-neurosynth Large-scale synthesis of functional neuroimaging data Needs packaging
python-dipy Diffusion MRI utilities in python Needs packaging
python-nipype Neuroimaging in Python: Pipelines and interfaces Needs packaging
sute2p Cell detection in calcium imaging recordings Needs packaging

Packages for Data Analysis

Package Summary Status Comment
openmeeg Low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG Packaged
python-mne Magnetoencephalography (MEG) and Electroencephalography (EEG) data analysis Packaged
python-pyactivetwo Python library for reading signal from BioSemi ActiveTwo EEG device Packaged
python-PyMVPA Multivariate pattern analysis Needs packaging. Dead review here: 1280485
python-pymc3 Bayesian statistical modeling and model fitting Needs packaging. Dead review here 1288870
python-pyspike Python library for the numerical analysis of spiketrain similarity Needs packaging. Dead review here: 1291061
python-epac Machine learning workflow builder In review 1293043
python-nitime Nitime is a library for time-series analysis of data from neuroscience experiments Needs packaging
PyMICE PyMICE is a Python library for mice behavioural data analysis. Needs packaging

Packages for Modeling of neural systems

Package Summary Status Comment
moose Multiscale Neuroscience and Systems Biology Simulator Packaged
nest NEST-The neural simulation tool Packaged
Brian The Brian spiking neural simulator Needs packaging, dead review 1098754
PyNN A Python package for simulator independent specification of neuronal network models Review ready, needs deps 1150105
The NEURON simulator Empirically based simulations of neurons and networks of neurons Needs packaging, dead review 1249094
MUSIC MUSIC, the MUltiSimulation Coordinator Needs packaging
NetPyNE A python package to facilitate the development of biological neuronal networks in NEURON Needs packaging, depends on NEURON
libneurosim Common interfaces for neuronal simulators Needs review 1638968
GENESIS GENESIS (the GEneral NEural SImulation System) is a general purpose simululation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and system-level models. COPR exists
example Packaged

Misc Libraries/Utilities

Package Summary Status Comment
python-neo Represent electrophysiology data in Python Packaged
DiffusionKurtosisFit Reconstruct Diffusion Kurtosis tensor from Diffusion Weighted MRI Packaged
getdp Finite element solver Packaged
gifticlib Refernce IO implementation and tools of the GIFTI XML based file format for cortical surface data Packaged
nipy-data Test data and brain templates for nipy Packaged
openigtlink Reference implementation of OpenIGTLink: a set of message formats and protocols used for data exchange over a local area network Packaged
petpvc Tools for partial volume correction (PVC) in positron emission tomography (PET) Packaged
python-amico Relationships backed by Redis Packaged
python-baker Easy, powerful access to Python functions from the command line Packaged
python-citeproc-py Citations and bibliography formatter Packaged
python-gradunwarp Gradient Unwarping Packaged
python-h5io Read and write simple Python objects using HDF5 Packaged
python-interfile Python module for read/write/parse interfile Packaged
python-klusta Spike detection and automatic clustering for spike sorting Packaged
python-lazyarray A lazily-evaluated numerical array class Packaged
python-moss Assorted utilities for neuroimaging and cognitive science Packaged
python-nixio Python bindings for NIX, the Neuroscience Exchange Format Packaged
python-pydotplus Python interface to Graphviz's Dot language Packaged
python-PyLink Universal communication interface using File-Like API Packaged
python-pyoptical Pure Python interface to OptiCAL Packaged
python-pyriemann Covariance matrices manipulaton and Biosignal classification Packaged
python-pyxid Python library for interfacing with Cedrus XID and StimTracker devices Packaged
python-quantities Support for physical quantities with units, based on numpy Packaged
python-simplewrap Easy to use wrappers generator for C libraries based on ctypes Packaged
python-tabulate Pretty-print tabular data in Python, a library and a command-line utility Packaged
python-transforms3d 3 dimensional spatial transformations Packaged
texlive The LaTeX typesetting system for academic writing Packaged
python-grabbit Get grabby with file trees! Packaged
python-cma Covariance Matrix Adaptation Evolution Strategy numerical optimizer Packaged
MorphoPy a Python 3 package for handling morphological reconstructions of neurons and computing summary statistics Needs packaging
Btmorph Small Python library containing a data structure and tools to represent and analyze neuronal morphologies stored in the de facto standard SWC format Needs packaging
python-psychopy Psychophysics toolkit for Python Needs packaging. A dead review is here: 1280141
python-cregg Utilities for running psychology experiments In review 1280155
python-duecredit Automated collection and reporting of citations for used software/methods/datasets Needs packaging. Dead review here: 1280480
python-visionegg-quest QUEST algorithm for finding threshold Reviewed: needs import 1290995
debruijn Software for the generation de Bruijn sequences for neuroscience experiments Needs packaging. Dead review here: 1291021
neuroshare Python bindings for Neuroshare Needs packaging
expyriment A Python library for cognitive and neuroscientific experiments Needs packaging
pyphi A Python package for computing integrated information Needs review: 1619458
pyemd Fast EMD for Python: a wrapper for Pele and Werman's C++ implementation of Earth Mover's Distance metric Needs packaging
uncertainpy A Python toolbox for uncertainty quantification and sensitivity analysis Needs packaging
nuitka A fully compatible Python compiler Needs packaging. Dead review here: 1288750
tridesclous offline/online spike sorting with french touch that light the barbecue Needs packaging