Packages for Ubuntu 16.04 “Xenial Xerus” (xenial)

afni

• afni (toolkit for analyzing and visualizing functional MRI data)

• afni-common (miscellaneous scripts and data files for AFNI)

• afni-dbg (debug symbols for AFNI)

• afni-dev (header and static libraries for AFNI plugin development)

afni-data

• afni-atlases (standard space brain atlases for AFNI)

aghermann

• aghermann (Sleep-research experiment manager)

ants

• ants (advanced normalization tools for brain and image analysis)

asciidoctor

• asciidoctor (AsciiDoc to HTML rendering for Ruby)

• asciidoctor-doc (AsciiDoc to HTML rendering for Ruby (documentation))

• ruby-asciidoctor (AsciiDoc to HTML rendering for Ruby (core libraries))

bats

• bats (bash automated testing system)

btrbk

• btrbk (backup tool for btrfs subvolumes)

cde

• cde (package everything required to execute a Linux command on another computer)

chardet

• python-chardet (universal character encoding detector for Python2)

• python3-chardet (universal character encoding detector for Python3)

cmtk

• cmtk (Computational Morphometry Toolkit)

cnrun

• cnrun-tools (NeuroML-capable neuronal network simulator (tools))

• libcnrun2 (NeuroML-capable neuronal network simulator (shared lib))

• libcnrun2-dev (NeuroML-capable neuronal network simulator (development files))

• lua-cnrun (NeuroML-capable neuronal network simulator (Lua package))

condor

• htcondor (distributed workload management system)

• htcondor-dbg (distributed workload management system - debugging symbols)

• htcondor-dev (distributed workload management system - development files)

• htcondor-doc (distributed workload management system - documentation)

• libclassad-dev (HTCondor classads expression language - development library)

• libclassad8 (HTCondor classads expression language - runtime library)

connectome-workbench

• connectome-workbench (brain visualization, analysis and discovery tool)

• connectome-workbench-dbg (brain visualization, analysis and discovery tool – debug symbols)

convert3d

• convert3d (tool(s) for converting 3D images between common file formats)

copyq

• copyq (Advanced clipboard manager with editing and scripting features)

• copyq-doc (Documentation and examples for CopyQ - HTML format)

• copyq-plugins (Plugins for CopyQ)

datalad

• datalad (data files management and distribution platform)

• python3-datalad (data files management and distribution platform)

datalad-container

• datalad-container (DataLad extension for working with containerized environments)

dcm2niix

• dcm2niix (converts DICOM and PAR/REC files into the NIfTI format)

dcmstack

• python3-dcmstack (DICOM to NIfTI conversion - python3 package)

debhelper

• debhelper (helper programs for debian/rules)

• libdebhelper-perl (debhelper perl modules)

debruijn

• debruijn (De Bruijn cycle generator)

dipy

• python-dipy (Python library for the analysis of diffusion MRI datasets)

• python-dipy-doc (Python library for the analysis of diffusion MRI datasets – documentation)

• python-dipy-lib (Python library for the analysis of diffusion MRI datasets – extensions)

diskcache

• python3-diskcache (Python module for Disk and file backed persistent cache)

docker-compose

• docker-compose (Punctual, lightweight development environments using Docker)

dockerpty

• python-dockerpty (Pseudo-tty handler for docker Python client (Python 2.x))

• python3-dockerpty (Pseudo-tty handler for docker Python client (Python 3.x))

drawtk

• libdrawtk-dev (Library to simple and efficient 2D drawings (development files))

• libdrawtk0 (Library to simple and efficient 2D drawings)

• libdrawtk0-dbg (Library to simple and efficient 2D drawings (debugging symbols))

duecredit

• python3-duecredit (Publications (and donations) tracer)

dwz

• dwz (DWARF compression tool)

eeglab11

• eeglab11-sampledata (sample EEG data for EEGLAB tutorials)

• matlab-eeglab11 (electrophysiological data analysis)

fail2ban

• fail2ban (ban hosts that cause multiple authentication errors)

fsl

• fsl (transitional dummy package)

• fsl-5.0 (transitional dummy package)

• fsl-5.0-core (analysis tools for FMRI, MRI and DTI brain imaging)

• fsl-core (metapackage for the latest version of FSL)

fsl-eddy-nonfree

• fsl-5.0-eddy-nonfree (correcting eddy currents and movements in diffusion data)

fsleyes

• fsleyes (FSL image viewer)

fsleyes-props

• python-fsleyes-props (Python descriptor framework)

fsleyes-widgets

• python-fsleyes-widgets (Python descriptor framework)

fslmeta

• fsl-5.0-complete (metapackage for the entire FSL suite (tools and data))

• fsl-complete (metapackage for the entire FSL suite (tools and data))

fslpy

• python-fsl (FSL Python library)

• python3-fsl (FSL Python library)

fslview

• fslview (viewer for (f)MRI and DTI data)

• fslview-doc (Documentation for FSLView)

gcalcli

• gcalcli (Google Calendar Command Line Interface)

gifticlib

• gifti-bin (tools shipped with the GIFTI library)

• libgiftiio-dev (IO library for the GIFTI cortical surface data format)

• libgiftiio0 (IO library for the GIFTI cortical surface data format)

git-annex

• git-annex-standalone (manage files with git, without checking their contents into git – standalone build)

git-annex-adapter

• python3-git-annex-adapter (call git-annex commands from within Python)

git-annex-metadata-gui

• git-annex-metadata-gui (graphical interface to the metadata functionality of git-annex)

git-annex-remote-rclone

• git-annex-remote-rclone (rclone-based git annex special remote)

git-hub

• git-hub (Git command line interface to GitHub)

heudiconv

• heudiconv (DICOM converter with support for structure heuristics)

impressive

• impressive (PDF presentation tool with eye candies)

incf-nidash-oneclick

• incf-nidash-oneclick-clients (utility for pushing DICOM data to the INCF datasharing server)

indexed-gzip

• python-indexed-gzip (fast random access of gzip files in Python)

• python3-indexed-gzip (fast random access of gzip files in Python)

ismrmrd

• ismrmrd-schema (ISMRM Raw Data format (ISMRMRD) - XML schema)

• ismrmrd-tools (ISMRM Raw Data format (ISMRMRD) - binaries)

• libismrmrd-dev (ISMRM Raw Data format (ISMRMRD) - development files)

• libismrmrd-doc (ISMRM Raw Data format (ISMRMRD) - documentation)

• libismrmrd1.3 (ISMRM Raw Data format (ISMRMRD) - shared library)

jasp

• jasp (Bayesian statistics made accessible)

joblib

• python-joblib (tools to provide lightweight pipelining in Python)

• python3-joblib (tools to provide lightweight pipelining in Python)

json-tricks

• pypy-json-tricks (Python module with extra features for JSON files)

• python-json-tricks (Python module with extra features for JSON files)

• python3-json-tricks (Python module with extra features for JSON files)

lda

• python-lda (Topic modeling with latent Dirichlet allocation for Python 3)

• python3-lda (Topic modeling with latent Dirichlet allocation)

libfreenect

• freenect (library for accessing Kinect device – metapackage)

• libfreenect-bin (library for accessing Kinect device – utilities and samples)

• libfreenect-demos (library for accessing Kinect device – dummy package)

• libfreenect-dev (library for accessing Kinect device – development files)

• libfreenect-doc (library for accessing Kinect device – documentation)

• libfreenect0.5 (library for accessing Kinect device)

melview

• fsl-melview (viewer for the output of FSL’s MELODIC)

mialmpick

• mialmpick (Tools for landmark picking in 3D volume data sets)

• mialmpick-dbg (Debug information landmark picking tool mialmpick)

mridefacer

• mridefacer (de-identification of MRI data)

mrtrix

• mrtrix (diffusion-weighted MRI white matter tractography)

• mrtrix-doc (documentation for mrtrix)

mrtrix3

• mrtrix3 (diffusion-weighted MRI white matter tractography)

• mrtrix3-doc (documentation for mrtrix3)

mutagen

• python-mutagen (audio metadata editing library)

• python-mutagen-doc (audio metadata editing library - documentation)

• python3-mutagen (audio metadata editing library (Python 3))

ncdu

• ncdu (ncurses disk usage viewer)

netselect

• netselect (speed tester for choosing a fast network server)

• netselect-apt (speed tester for choosing a fast Debian mirror)

neurodebian

• neurodebian (neuroscience-oriented distribution - repository configuration)

• neurodebian-archive-keyring (neuroscience-oriented distribution - GnuPG archive keys)

• neurodebian-desktop (neuroscience-oriented distribution - desktop integration)

• neurodebian-dev (neuroscience-oriented distribution - development tools)

• neurodebian-freeze (nd_freeze tool to freeze APT sources to use snapshots)

• neurodebian-popularity-contest (neuroscience-oriented distribution - popcon integration)

neurosynth

• python-neurosynth (large-scale synthesis of functional neuroimaging data)

nibabel

• python-nibabel-doc (documentation for NiBabel)

• python3-nibabel (Python3 bindings to various neuroimaging data formats)

nilearn

• python-nilearn (fast and easy statistical learning on neuroimaging data (Python 2))

• python3-nilearn (fast and easy statistical learning on neuroimaging data (Python 3))

nipy

• python-nipy-doc (documentation and examples for NiPy)

• python3-nipy (Analysis of structural and functional neuroimaging data)

• python3-nipy-lib (Analysis of structural and functional neuroimaging data (compiled modules))

• python3-nipy-lib-dbg (Analysis of structural and functional neuroimaging data (debug symbols))

nipype

• python-nipype-doc (Neuroimaging data analysis pipelines in Python3 – documentation)

• python3-nipype (Neuroimaging data analysis pipelines in Python3)

nitime

• python-nitime-doc (timeseries analysis for neuroscience data (nitime) – documentation)

• python3-nitime (timeseries analysis for neuroscience data (nitime))

nuitka

• nuitka (Python compiler with full language support and CPython compatibility)

numdiff

• numdiff (Compare similar files with numeric fields)

numexpr

• python-numexpr (Fast numerical array expression evaluator for Python and NumPy)

• python3-numexpr (Fast numerical array expression evaluator for Python 3 and NumPy)

openpyxl

• python-openpyxl (Python module to read/write OpenXML xlsx/xlsm files)

• python3-openpyxl (Python 3 module to read/write OpenXML xlsx/xlsm files)

openstack-pkg-tools

• openstack-pkg-tools (Tools and scripts for building Openstack packages in Debian)

p7zip

• p7zip (7zr file archiver with high compression ratio)

• p7zip-full (7z and 7za file archivers with high compression ratio)

pandas

• python-pandas (data structures for “relational” or “labeled” data)

• python-pandas-doc (documentation and examples for pandas)

• python-pandas-lib (low-level implementations and bindings for pandas)

• python3-pandas (data structures for “relational” or “labeled” data - Python 3)

• python3-pandas-lib (low-level implementations and bindings for pandas - Python 3)

patool

• patool (command line archive file manager)

patsy

• python-patsy (statistical models in Python using symbolic formulas)

• python-patsy-doc (documentation and examples for patsy)

• python3-patsy (statistical models in Python using symbolic formulas)

pprocess

• python-pprocess (elementary parallel programming for Python)

props

• python-props (Python descriptor framework)

psychopy

• psychopy (environment for creating psychology stimuli in Python)

psychtoolbox-3

• octave-psychtoolbox-3 (toolbox for vision research – Octave bindings)

• psychtoolbox-3-common (toolbox for vision research – arch/interpreter independent part)

• psychtoolbox-3-dbg (toolbox for vision research – debug symbols for binaries)

• psychtoolbox-3-lib (toolbox for vision research – arch-specific parts)

psychtoolbox-3-nonfree

• matlab-psychtoolbox-3 (toolbox for vision research – Matlab bindings)

• matlab-psychtoolbox-3-nonfree (toolbox for vision research – Matlab binary blobs)

• octave-psychtoolbox-3-nonfree (toolbox for vision research – Octave binary blobs)

pycharm-community-sloppy

• pycharm-community-sloppy (PyCharm IDE (sloppy packaging))

pydot

• python-pydot (Python interface to Graphviz’s dot)

• python3-pydot (Python interface to Graphviz’s dot (Python 3))

pyepl

• python-pyepl (module for coding psychology experiments in Python)

• python-pyepl-common (module for coding psychology experiments in Python)

pygithub

• python3-github (Access the full Github API v3 from Python3)

pyglet

• python3-pyglet (cross-platform windowing and multimedia library (Python 3))

pymvpa2

• python-mvpa2 (multivariate pattern analysis with Python v. 2)

• python-mvpa2-doc (documentation and examples for PyMVPA v. 2)

• python-mvpa2-lib (low-level implementations and bindings for PyMVPA v. 2)

pyopengl

• python-opengl (Python bindings to OpenGL (Python 2))

• python3-opengl (Python bindings to OpenGL (Python 3))

pysurfer

• python-surfer (visualize Freesurfer’s data in Python)

pytest

• pypy-pytest (Simple, powerful testing in PyPy)

• python-pytest (Simple, powerful testing in Python)

• python-pytest-doc (Simple, powerful testing in Python - Documentation)

• python3-pytest (Simple, powerful testing in Python3)

pytest-runner

• python-pytest-runner (Invoke py.test as distutils command with dependency resolution)

• python3-pytest-runner (Invoke py.test as distutils command with dependency resolution)

python-argcomplete

• python3-argcomplete (bash tab completion for argparse (for Python 3))

python-babel

• python-babel (tools for internationalizing Python applications - Python 2.x)

• python-babel-doc (tools for internationalizing Python applications - documentation)

• python-babel-localedata (tools for internationalizing Python applications - locale data files)

• python3-babel (tools for internationalizing Python applications - Python 3.x)

python-boto

• python-boto (Python interface to Amazon’s Web Services - Python 2.x)

• python3-boto (Python interface to Amazon’s Web Services - Python 3.x)

python-boto3

• python-boto3 (Python interface to Amazon’s Web Services - Python 2.x)

• python3-boto3 (Python interface to Amazon’s Web Services - Python 3.x)

python-bz2file

• python-bz2file (Python library for reading and writing bzip2-compressed files)

• python3-bz2file (Python3 library for reading and writing bzip2-compressed files)

python-click

• python-click (Simple wrapper around optparse for powerful command line utilities - Python 2.7)

• python3-click (Simple wrapper around optparse for powerful command line utilities - Python 3.x)

python-deprecation

• python-deprecation (Library to handle automated deprecations - Python 2.x)

• python3-deprecation (Library to handle automated deprecations - Python 3.x)

python-docker

• python-docker (Python wrapper to access docker.io’s control socket)

• python3-docker (Python 3 wrapper to access docker.io’s control socket)

python-exif

• python-exif (Python library to extract Exif data from TIFF and JPEG files)

• python3-exif (Python library to extract Exif data from TIFF and JPEG files)

python-fasteners

• python3-fasteners (provides useful locks - Python 3.x)

python-funcsigs

• python-funcsigs (function signatures from PEP362 - Python 2.7)

• python-funcsigs-doc (function signatures from PEP362 - doc)

• python3-funcsigs (function signatures from PEP362 - Python 3.x)

python-git

• python-git-doc (Python library to interact with Git repositories - docs)

• python3-git (Python library to interact with Git repositories - Python 3.x)

python-gitdb

• python-gitdb (pure-Python git object database (Python 2))

• python3-gitdb (pure-Python git object database (Python 3))

python-httpretty

• python3-httpretty (HTTP client mock - Python 3.x)

python-hypothesis

• pypy-hypothesis (advanced Quickcheck style testing library for PyPy)

• python-hypothesis (advanced Quickcheck style testing library for Python 2)

• python-hypothesis-doc (advanced Quickcheck style testing library (documentation))

• python3-hypothesis (advanced Quickcheck style testing library for Python 3)

python-jsmin

• python-jsmin (JavaScript minifier written in Python - Python 2.x)

• python3-jsmin (JavaScript minifier written in Python - Python 3.x)

python-mne

• python-mne (Python modules for MEG and EEG data analysis)

python-monotonic

• python-monotonic (implementation of time.monotonic() - Python 2.x)

• python3-monotonic (implementation of time.monotonic() - Python 3.x)

python-prov

• prov-tools (tools for prov)

• python-prov (W3C Provenance Data Model (Python 2))

• python-prov-doc (documentation for prov)

• python3-prov (W3C Provenance Data Model (Python 3))

python-py

• pypy-py (Advanced Python development support library (PyPy))

• python-py (Advanced Python development support library (Python 2))

• python3-py (Advanced Python development support library (Python 3))

python-pydotplus

• python-pydotplus (interface to Graphviz’s Dot language - Python 2.7)

• python-pydotplus-doc (interface to Graphviz’s Dot language - doc)

• python3-pydotplus (interface to Graphviz’s Dot language - Python 3.x)

python-pygraphviz

• python-pygraphviz (Python interface to the Graphviz graph layout and visualization package)

• python-pygraphviz-dbg (Python interface to the Graphviz graph layout and visualization package (debug extension))

• python-pygraphviz-doc (Python interface to the Graphviz graph layout and visualization package (doc))

• python3-pygraphviz (Python interface to the Graphviz graph layout and visualization package (Python 3))

• python3-pygraphviz-dbg (Python interface to the Graphviz graph layout and visualization package (py3k debug extension))

python-pyperclip

• python-pyperclip (Cross-platform clipboard module for Python)

• python3-pyperclip (Cross-platform clipboard module for Python3)

python-setuptools

• pypy-pkg-resources (Package Discovery and Resource Access using pkg_resources)

• pypy-setuptools (PyPy Distutils Enhancements)

• python-pkg-resources (Package Discovery and Resource Access using pkg_resources)

• python-setuptools (Python Distutils Enhancements)

• python-setuptools-doc (Python Distutils Enhancements (documentation))

• python3-pkg-resources (Package Discovery and Resource Access using pkg_resources)

• python3-setuptools (Python3 Distutils Enhancements)

python-smmap

• python-smmap (pure Python implementation of a sliding window memory map manager)

• python3-smmap (pure Python implementation of a sliding window memory map manager)

python-urllib3

• python-urllib3 (HTTP library with thread-safe connection pooling for Python)

• python-urllib3-whl (HTTP library with thread-safe connection pooling)

• python3-urllib3 (HTTP library with thread-safe connection pooling for Python3)

python-whoosh

• python-whoosh (pure-Python full-text indexing, search, and spell checking library (Python 2))

• python-whoosh-doc (full-text indexing, search, and spell checking library (doc))

• python3-whoosh (pure-Python full-text indexing, search, and spell checking library (Python 3))

python-wrapt

• python-wrapt (decorators, wrappers and monkey patching. - Python 2.x)

• python-wrapt-doc (decorators, wrappers and monkey patching. - doc)

• python3-wrapt (decorators, wrappers and monkey patching. - Python 3.x)

python-xmp-toolkit

• python3-libxmp (Python3 library for XMP metadata)

• python3-libxmp-doc (Python library for XMP metadata - documentation)

rclone

• golang-github-ncw-rclone-dev (go source code of rclone)

• rclone (rsync for commercial cloud storage)

remake

• remake (GNU make fork with improved error reporting and debugging)

requests

• python-requests (elegant and simple HTTP library for Python2, built for human beings)

• python-requests-whl (elegant and simple HTTP library for Python, built for human beings)

• python3-requests (elegant and simple HTTP library for Python3, built for human beings)

scikit-learn

• python-sklearn (Python modules for machine learning and data mining)

• python-sklearn-doc (documentation and examples for scikit-learn)

• python-sklearn-lib (low-level implementations and bindings for scikit-learn)

• python3-sklearn (Python modules for machine learning and data mining - Python 3)

• python3-sklearn-lib (low-level implementations and bindings for scikit-learn - Python 3)

seaborn

• python-seaborn (statistical visualization library)

• python3-seaborn (statistical visualization library)

singularity-container

• singularity-container (container platform focused on supporting “Mobility of Compute”)

six

• pypy-six (Python 2 and 3 compatibility library (PyPy interface))

• python-six (Python 2 and 3 compatibility library (Python 2 interface))

• python3-six (Python 2 and 3 compatibility library (Python 3 interface))

solar-eclipse

• solar-eclipse (genetic variance components analysis software)

sparql-wrapper-python

• python-sparqlwrapper (SPARQL endpoint interface to Python)

• python3-sparqlwrapper (SPARQL endpoint interface to Python3)

sphinx-gallery

• python-sphinx-gallery (extension that builds an HTML gallery of examples from Python scripts)

• python-sphinx-gallery-doc (extension that builds an HTML gallery of examples from Python scripts (Doc))

• python3-sphinx-gallery (extension that builds an HTML gallery of examples from Python scripts (Python 3))

spm8

• matlab-spm8 (analysis of brain imaging data sequences for Matlab)

• spm8-common (analysis of brain imaging data sequences)

• spm8-data (data files for SPM8)

• spm8-doc (manual for SPM8)

statsmodels

• python-statsmodels (Python module for the estimation of statistical models)

• python-statsmodels-doc (documentation and examples for statsmodels)

• python-statsmodels-lib (low-level implementations and bindings for statsmodels)

• python3-statsmodels (Python3 module for the estimation of statistical models)

• python3-statsmodels-lib (Python3 low-level implementations and bindings for statsmodels)

stimfit

• python-stfio (Python module to read common electrophysiology file formats.)

• stimfit (Program for viewing and analyzing electrophysiological data)

• stimfit-dbg (Debug symbols for stimfit)

tqdm

• python-tqdm (fast, extensible progress bar for Python 2)

• python3-tqdm (fast, extensible progress bar for Python 3 and CLI tool)

ubuntu-keyring

• ubuntu-keyring (GnuPG keys of the Ubuntu archive)

• ubuntu-keyring-udeb ()

uftp

• uftp (Encrypted multicast file transfer program)

utopia-documents

• utopia-documents (PDF reader that displays interactive annotations on scientific articles)

• utopia-documents-dbg (debugging symbols for utopia-documents)

vcr.py

• python-vcr (record and replay HTML interactions (Python library))

• python3-vcr (record and replay HTML interactions (Python3 library))

vmri-nonfree

• virtual-mri-nonfree (Virtual Magnetic Resonance Imager)

vowpal-wabbit

• libvw-dev (fast and scalable online machine learning algorithm - development files)

• libvw0 (fast and scalable online machine learning algorithm - dynamic library)

• vowpal-wabbit (fast and scalable online machine learning algorithm)

• vowpal-wabbit-dbg (fast and scalable online machine learning algorithm - debug files)

• vowpal-wabbit-doc (fast and scalable online machine learning algorithm - documentation)

vrpn

• libvrpn-dev (Virtual Reality Peripheral Network (development files))

• libvrpn0 (Virtual Reality Peripheral Network (client library))

• libvrpnserver0 (Virtual Reality Peripheral Network (server library))

• vrpn (Virtual Reality Peripheral Network (executables))

• vrpn-dbg (Virtual Reality Peripheral Network (debugging symbols))

vtk-dicom

• libvtk-dicom-java (DICOM for VTK - java)

• libvtk-dicom0.5 (DICOM for VTK - lib)

• libvtk-dicom0.5-dev (DICOM for VTK - dev)

• python-vtk-dicom (DICOM for VTK - python)

• vtk-dicom-tools (DICOM for VTK - tools)

youtube-dl

• youtube-dl (downloader of videos from YouTube and other sites)

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