Packages for Ubuntu 18.04 “Bionic Beaver” (bionic)

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)

annexremote

• python3-annexremote (abstraction for git-annex special remote implementations)

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)

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))

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)

dask

• python-dask-doc (Minimal task scheduling abstraction documentation)

• python3-dask (Minimal task scheduling abstraction for Python 3)

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)

dh-octave

• dh-octave (Debhelper-based infrastructure for building Octave add-on packages)

• dh-octave-autopkgtest (script for the automatic testing of Octave add-on packages)

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)

duecredit

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

dwz

• dwz (DWARF compression tool)

edac-utils

• edac-utils (report kernel-detected PCI and ECC RAM errors)

• libedac-dev (report kernel-detected PCI and ECC RAM errors)

• libedac1 (report kernel-detected PCI and ECC RAM errors)

• libedac1-dbg (report kernel-detected PCI and ECC RAM errors)

exempi

• exempi (command line tool to manipulate XMP metadata)

• libexempi-dev (library to parse XMP metadata (Development files))

• libexempi3 (library to parse XMP metadata (Library))

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)

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)

git

• git (fast, scalable, distributed revision control system)

• git-all (fast, scalable, distributed revision control system (all subpackages))

• git-cvs (fast, scalable, distributed revision control system (cvs interoperability))

• git-daemon-run (fast, scalable, distributed revision control system (git-daemon service))

• git-daemon-sysvinit (fast, scalable, distributed revision control system (git-daemon service))

• git-doc (fast, scalable, distributed revision control system (documentation))

• git-el (fast, scalable, distributed revision control system (emacs support))

• git-email (fast, scalable, distributed revision control system (email add-on))

• git-gui (fast, scalable, distributed revision control system (GUI))

• git-man (fast, scalable, distributed revision control system (manual pages))

• git-mediawiki (fast, scalable, distributed revision control system (MediaWiki remote helper))

• git-svn (fast, scalable, distributed revision control system (svn interoperability))

• gitk (fast, scalable, distributed revision control system (revision tree visualizer))

• gitweb (fast, scalable, distributed revision control system (web interface))

git-annex

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

git-annex-remote-rclone

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

glm

• libglm-dev (C++ library for OpenGL GLSL type-based mathematics)

• libglm-doc (documentation for the OpenGL Mathematics (GLM) library)

hdmf

• python3-hdmf (Hierarchical Data Modeling Framework)

heudiconv

• heudiconv (DICOM converter with support for structure heuristics)

indexed-gzip

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

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

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)

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)

libqtpas

• libqt5pas-dev (Development files for Qt5Pas)

• libqt5pas1 (Qt5 interface bindings for Pascal)

melview

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

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)

msgpack-python

• python-msgpack (Python implementation of MessagePack format)

• python3-msgpack (Python 3 implementation of MessagePack format)

ncdu

• ncdu (ncurses disk usage viewer)

neo

• python3-neo (Python IO library for electrophysiological data formats)

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)

nibabel

• python-nibabel-doc (documentation for NiBabel)

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

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)

openstack-pkg-tools

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

openxr-sdk-source

• libopenxr-dev (OpenXR software development kit – development headers)

• libopenxr-loader1 (OpenXR loader library)

• libopenxr-utils (OpenXR software development kit – utilities)

• openxr-layer-apidump (OpenXR software development kit – API dump layer)

• openxr-layer-corevalidation (OpenXR software development kit – validation layer)

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)

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))

pydicom

• python-dicom (transitional package for python-pydicom)

• python-pydicom (DICOM medical file reading and writing (Python 2))

• python-pydicom-doc (DICOM medical file reading and writing (documentation))

• python3-dicom (transitional package for python3-pydicom)

• python3-pydicom (DICOM medical file reading and writing (Python 3))

pydot

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

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

pygithub

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

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)

pynwb

• python3-pynwb (Python library for working with Neurodata in the NWB format)

pyrsistent

• python3-pyrsistent (persistent/functional/immutable data structures for Python)

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-bz2file

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

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

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-filelock

• python-filelock (platform independent file locking module (Python 2))

• python3-filelock (platform independent file locking module (Python 3))

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-importlib-metadata

• python3-importlib-metadata (library to access the metadata for a Python package - Python 3.x)

python-jsonschema

• python-jsonschema-doc (An(other) implementation of JSON Schema (Draft 3 and 4) - doc)

• python3-jsonschema (An(other) implementation of JSON Schema (Draft 3 and 4) - Python 3.x)

python-pyfakefs

• python3-pyfakefs (fake fs that mocks the Python file system modules - Python 3)

python-pyperclip

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

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

python-quantities

• python3-quantities (Library for computation of physical quantities with units, based on numpy)

python-sphinxcontrib.apidoc

• python3-sphinxcontrib.apidoc (Sphinx extension for running ‘sphinx-apidoc’ on each build - Python 3.x)

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-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)

python-zipp

• python3-zipp (pathlib-compatible Zipfile object wrapper - Python 3.x)

pyxid

• python3-pyxid (interface for Cedrus XID and StimTracker devices)

rclone

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

• rclone (rsync for commercial cloud storage)

reprozip

• python3-reprozip (modules for the ReproZip packer)

• python3-reprozip-dbg (debug extensions for the ReproZip packer)

• reprozip (tool for reproducing scientific experiments (packer))

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)

s3cmd

• s3cmd (command-line Amazon S3 client)

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)

singularity-container

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

skimage

• python-skimage (Python modules for image processing)

• python-skimage-doc (Documentation and examples for scikit-image)

• python-skimage-lib (Optimized low-level algorithms for scikit-image)

• python3-skimage (Python 3 modules for image processing)

• python3-skimage-lib (Optimized low-level algorithms for Python 3 scikit-image)

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))

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)

svgtune

• svgtune (tool to generate a set of .svg files out of a single .svg file)

sympy

• isympy-common (Python shell for SymPy)

• isympy3 (Python3 shell for SymPy)

• python-sympy (Computer Algebra System (CAS) in Python)

• python-sympy-doc (Computer Algebra System (CAS) in Python - Documentation)

• python3-sympy (Computer Algebra System (CAS) in Python (Python3))

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)

xlwt

• python-xlwt (module for writing Microsoft Excel spreadsheet files - Python 2.7)

• python-xlwt-doc (module for writing Microsoft Excel spreadsheet files - doc)

• python3-xlwt (module for writing Microsoft Excel spreadsheet files - Python 3.x)

youtube-dl

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

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