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reduced the number of required packages, most of them are not really …
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…required for now
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@JohannesWiesner
JohannesWiesner committed Nov 2, 2023
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package_name version installation_command package_manager conda_channel area link necessity description comment language bug_flag
pyarrow conda install -c conda-forge pyarrow conda conda-forge data wrangling https://arrow.apache.org/docs/python/install.html optional pyarrow is required to save pandas data frames as .feather files (which is the format to exchange data between python and R) Not recommended to install that, because the 'R-side' of this version can not be installed on the CIMH servers (not sure if this issue still exists). Besides, one can also use rpy2 to exchange files. Python cross-platform
xmltodict pip install xmltodict pip data wrangling https://pypi.org/project/xmltodict/ optional working with xml files this is required for Johannes pycat library Python
yellowbrick conda install -c districtdatalabs yellowbrick conda districtdatalabs plotting https://www.scikit-yb.org/en/latest/index.html optional Builds upon seaborn and has some advanced plotting classes such as Radviz (https://www.scikit-yb.org/en/latest/api/features/radviz.html) Python
dash conda install -c conda-forge dash conda conda-forge plotting https://dash.plotly.com/introduction optional Used for nct_tutorial from Johannes Python
dash-bootstrap-components conda install -c conda-forge dash-bootstrap-components conda conda-forge plotting https://dash-bootstrap-components.opensource.faculty.ai/docs/quickstart/ optional Used for nct_tutorial from Johannes Allows to create dash-apps using a grid-layout (e.g. rows and columns) Python
adjustText pip install adjustText pip plotting https://github.com/JohannesWiesner/pycat/blob/master/pycat.py optional adjust text in matplotlib figures Python
dash-cytoscape pip install dash-cytoscape pip plotting https://dash.plotly.com/cytoscape optional Used for nct_tutorial from Johannes Allows to plot networks in dash Python
brainrender pip install brainrender pip plotting https://github.com/brainglobe/brainrender optional plotting 3D brains Python
semopy pip install semopy pip statistical modelling https://semopy.com/ optional Used for structural equation modelling in python Bug: scikit-learn has now to be installed as scikit-learn, not sklearn (https://gitlab.com/georgy.m/semopy/-/issues/35), once issue is solved we can re-include semopy again Python
gemmr pip install gemmr pip statistical modelling https://github.com/murraylab/gemmr optional A library that allows you to use Witten et als. PMA function via rpy2 Python
resample pip install resample pip statistical modelling https://github.com/scikit-hep/resample optional Allows you to do permutation and bootstrapping resampling This requires a C-compiler to be installed on your machine. On CIMH machines this can be tedious to install Python cross-platform
pytorch conda install -c pytorch pytorch conda pytorch machine learning https://anaconda.org/pytorch/pytorch optional Tensor library for deep learning using GPUs and CPUs Python
tensorboardx conda install -c conda-forge tensorboardx conda conda-forge machine learning https://anaconda.org/conda-forge/tensorboardx optional Allows researchers to use simple interface to log events within PyTorch Python
neurokit2 conda install -c conda-forge neurokit2 conda conda-forge statistical modelling https://github.com/neuropsychology/NeuroKit optional NeuroKit2 is a user-friendly package providing easy access to advanced biosignal processing routines This package is specifically needed to compute multiscale sample entropy (there are also other packages though, that can do this or might include this in the future which are also smaller: https://github.com/nikdon/pyEntropy, https://github.com/ELIFE-ASU/PyInform) Python
fmriprep-docker pip install fmriprep-docker pip neuroimaging https://fmriprep.org/en/20.2.0/installation.html#the-fmriprep-docker-wrapper optional This package makes the invocation of fmriprep easier Python
jupyter-book conda install -c conda-forge jupyter-book conda conda-forge ide https://jupyterbook.org/en/stable/intro.html optional Used for creating workshop webpages. Not needed for any data analysis Python
nimare pip install nimare pip statistical modelling https://nimare.readthedocs.io/en/stable/ required Used to derive statistical images from neurosynth.org Python
python <3.10 conda install -c conda-forge python conda conda-forge language https://anaconda.org/conda-forge/python required the python programming language itself Python
sklearn-pandas conda install -c conda-forge sklearn-pandas conda conda-forge data wrangling https://github.com/scikit-learn-contrib/sklearn-pandas optional Nötig, um scikit-learn transfomer direkt auf pandas data frames anzuwenden Python
datalad conda install -c conda-forge datalad conda conda-forge data wrangling https://www.datalad.org/ required Allows you to download and manage datalad datasets https://www.datalad.org/ Python
tableone conda install -c conda-forge tableone conda conda-forge data wrangling https://github.com/tompollard/tableone required Package for plotting descriptive statistics Python
plotly-orca conda install -c plotly plotly-orca conda plotly dependency https://plotly.com/python/orca-management/ required Optional addon for plotly to export static images Plotly people now recommend to use kaleido instead (https://plotly.com/python/static-image-export/). So this should be changed to kaleido Python
Expand All @@ -36,9 +19,9 @@ network_control pip install network_control pip statistical modelling https://
cca-zoo pip install cca-zoo pip statistical modelling https://cca-zoo.readthedocs.io/en/latest/index.html required implementing canonical correlation analysis in python Python
bctpy pip install btcpy pip statistical modelling https://github.com/aestrivex/bctpy required A library that allows you to compute all sorts of topological measures on connectivity matrices Python
gower pip install gower pip statistical modelling https://pypi.org/project/gower/ required A package that allows you to compute Gower Distance Matrices Python
antropy pip install antropy pip statistical modelling https://github.com/raphaelvallat/antropy required AntroPy is a Python 3 package providing several time-efficient algorithms for computing the complexity of time-series. Python
mne conda install -c conda-forge mne conda conda-forge statistical modelling https://mne.tools/stable/index.html required Python package for analyzing MEG/EEG data Python
pyvis pip install pyvis pip plotting https://pyvis.readthedocs.io/en/latest/index.html required Visualizing graphs/networks in an interactive fashion This will automatically install networkx as a dependency Python
antropy pip install antropy pip statistical modelling https://github.com/raphaelvallat/antropy optional AntroPy is a Python 3 package providing several time-efficient algorithms for computing the complexity of time-series. Python
mne conda install -c conda-forge mne conda conda-forge statistical modelling https://mne.tools/stable/index.html optional Python package for analyzing MEG/EEG data Python
pyvis pip install pyvis pip plotting https://pyvis.readthedocs.io/en/latest/index.html optional Visualizing graphs/networks in an interactive fashion This will automatically install networkx as a dependency Python
distro pip install distro pip system https://pypi.org/project/distro/ required distro provides information about the OS distribution it runs on, such as a reliable machine-readable ID, or version information. This package is useful to detect on which specific distro your current python script is running. For example you might want to run the script both on your personal machine and on the server. In this case paths might change and you want to have an option to automatically change paths by detecting the OS Python
abagen pip install abagen pip statistical modelling https://abagen.readthedocs.io/en/stable/installation.html required abagen lets you get information about gene receptor densities using the Allen Human Brain Atlas and a custom atlas of your choice Python
oct2py conda install -c conda-forge oct2py conda conda-forge system https://pypi.org/project/oct2py/ required Oct2py allows use to run Octave from Python (so you can execute .m files) Python
Expand All @@ -47,13 +30,6 @@ groupyr pip install groupyr pip statistical modelling https://richiehalford.or
clustergrammer pip install clustergrammer pip plotting https://clustergrammer.readthedocs.io/clustergrammer_py.html required Let’s you create interactive clustermaps Python
nisupply pip install nisupply pip data wrangling https://github.com/JohannesWiesner/nisupply required Johannes Wiesner’s repository to deal with unstructured neuroimaging datasets Python
pybids conda install -c conda-forge pybids conda conda-forge data wrangling https://bids-standard.github.io/pybids/ required Pybids helps to query BIDS-datasets Python
arrow conda install -c conda-forge --strict-channel-priority r-arrow conda conda-forge data wrangling https://arrow.apache.org/docs/r/ optional Note: This currently seems to work for Windows but struggles with installation on Linux! Arrow is required to save data frames as .feather files (which is the format to exchange data between python and R). This documented error happens on the server: https://arrow.apache.org/docs/r/articles/install.html#package-failed-to-build-c-dependencies R cross-platform
r-matrixstats conda install -c conda-forge r-matrixstats conda conda-forge data wrangling https://anaconda.org/conda-forge/r-matrixstats optional required for reproducing Xia et al. CCA analysis R
r-pma conda install -c conda-forge r-pma conda conda-forge statistical modelling https://anaconda.org/conda-forge/r-pma optional Package to conduct sparse canonical correlation analysis Why do I added this? This is the same as install.packages('PMA') that can also be found in this spreadsheet? Choose either this package or install PMA package with CRAN, but not both. If you can succesfully use the gemmr package and if you can rerun Xia et al. script, then you don't have to use install.package('PMA'') R
PMA install.packages('PMA') cran statistical modelling https://cran.r-project.org/web/packages/PMA/index.html optional required for reproducing Xia et al. CCA analysis R
lme4 install.packages('lme4') cran statistical modelling https://cran.r-project.org/web/packages/lme4/lme4.pdf optional Fitting mixed models in R Note, that when using the python package pymer4, you will already have lme4 installed, so this installation would become obsolete. You might also need to install stamod (https://community.rstudio.com/t/error-message-when-trying-to-install-lmer-package-and-load-lmer-library/85418) R
r-dendextend conda install -c conda-forge r-dendextend conda conda-forge plotting https://r-charts.com/part-whole/circular-dendrogram/ optional Allows to customize dendrograms (e.g. coloring branches, adding labels) Should be installed together with circlize R
r-circlize conda install -c conda-forge r-circlize conda conda-forge plotting https://r-charts.com/part-whole/circular-dendrogram/ optional Allows to draw circular dendrograms Should be installed together with dendextend R
r-essentials conda install -c conda-forge r-essentials conda conda-forge data wrangling https://tinyurl.com/54j96j5x required The R Essentials bundle contains approximately 200 of the most popular R packages for data science, including the IRKernel, dplyr, shiny, ggplot2, tidyr, caret, and nnet. It is used as an example in the following guides. R
r-repr conda install -c conda-forge r-repr conda conda-forge dependency https://anaconda.org/conda-forge/r-repr required This is required if you want to use the Variable Inspector from Jupyter-Lab to be able to inspect R-objects https://github.com/lckr/jupyterlab-variableInspector#requirements-for-r-functionality R
rtools conda install -c r rtools conda r dependency https://anaconda.org/r/rtools required Why do I added this? Check why exactly this has to be installed. Current hypothesis: This is needed for devtools.This package is necessary to be able to install R-packages from GitHub. This package is not available in Linux R linux
Expand All @@ -64,3 +40,27 @@ jupyterlab conda install -c conda-forge jupyterlab conda conda-forge ide https:
r-base conda install -c conda-forge r-base conda conda-forge language https://anaconda.org/conda-forge/r-base required the R programming language itself R
r-reticulate conda install -c conda-forge r-reticulate conda conda-forge data wrangling https://cran.r-project.org/web/packages/RcppCNPy/vignettes/UsingReticulate.pdf required reticulate allows you to read in data generated from Python (e.g. .npy files) R
scikit-image conda install -c conda-forge scikit-image conda conda-forge statistical modelling https://scikit-image.org/ required We need that for otsu thresholding Python
pyarrow conda install -c conda-forge pyarrow conda conda-forge data wrangling https://arrow.apache.org/docs/python/install.html optional pyarrow is required to save pandas data frames as .feather files (which is the format to exchange data between python and R) Not recommended to install that, because the 'R-side' of this version can not be installed on the CIMH servers (not sure if this issue still exists). Besides, one can also use rpy2 to exchange files. Python cross-platform
xmltodict pip install xmltodict pip data wrangling https://pypi.org/project/xmltodict/ optional working with xml files this is required for Johannes pycat library Python
yellowbrick conda install -c districtdatalabs yellowbrick conda districtdatalabs plotting https://www.scikit-yb.org/en/latest/index.html optional Builds upon seaborn and has some advanced plotting classes such as Radviz (https://www.scikit-yb.org/en/latest/api/features/radviz.html) Python
dash conda install -c conda-forge dash conda conda-forge plotting https://dash.plotly.com/introduction optional Used for nct_tutorial from Johannes Python
dash-bootstrap-components conda install -c conda-forge dash-bootstrap-components conda conda-forge plotting https://dash-bootstrap-components.opensource.faculty.ai/docs/quickstart/ optional Used for nct_tutorial from Johannes Allows to create dash-apps using a grid-layout (e.g. rows and columns) Python
adjustText pip install adjustText pip plotting https://github.com/JohannesWiesner/pycat/blob/master/pycat.py optional adjust text in matplotlib figures Python
dash-cytoscape pip install dash-cytoscape pip plotting https://dash.plotly.com/cytoscape optional Used for nct_tutorial from Johannes Allows to plot networks in dash Python
brainrender pip install brainrender pip plotting https://github.com/brainglobe/brainrender optional plotting 3D brains Python
semopy pip install semopy pip statistical modelling https://semopy.com/ optional Used for structural equation modelling in python Bug: scikit-learn has now to be installed as scikit-learn, not sklearn (https://gitlab.com/georgy.m/semopy/-/issues/35), once issue is solved we can re-include semopy again Python
gemmr pip install gemmr pip statistical modelling https://github.com/murraylab/gemmr optional A library that allows you to use Witten et als. PMA function via rpy2 Python
resample pip install resample pip statistical modelling https://github.com/scikit-hep/resample optional Allows you to do permutation and bootstrapping resampling This requires a C-compiler to be installed on your machine. On CIMH machines this can be tedious to install Python cross-platform
pytorch conda install -c pytorch pytorch conda pytorch machine learning https://anaconda.org/pytorch/pytorch optional Tensor library for deep learning using GPUs and CPUs Python
tensorboardx conda install -c conda-forge tensorboardx conda conda-forge machine learning https://anaconda.org/conda-forge/tensorboardx optional Allows researchers to use simple interface to log events within PyTorch Python
neurokit2 conda install -c conda-forge neurokit2 conda conda-forge statistical modelling https://github.com/neuropsychology/NeuroKit optional NeuroKit2 is a user-friendly package providing easy access to advanced biosignal processing routines This package is specifically needed to compute multiscale sample entropy (there are also other packages though, that can do this or might include this in the future which are also smaller: https://github.com/nikdon/pyEntropy, https://github.com/ELIFE-ASU/PyInform) Python
fmriprep-docker pip install fmriprep-docker pip neuroimaging https://fmriprep.org/en/20.2.0/installation.html#the-fmriprep-docker-wrapper optional This package makes the invocation of fmriprep easier Python
jupyter-book conda install -c conda-forge jupyter-book conda conda-forge ide https://jupyterbook.org/en/stable/intro.html optional Used for creating workshop webpages. Not needed for any data analysis Python
sklearn-pandas conda install -c conda-forge sklearn-pandas conda conda-forge data wrangling https://github.com/scikit-learn-contrib/sklearn-pandas optional Nötig, um scikit-learn transfomer direkt auf pandas data frames anzuwenden Python
arrow conda install -c conda-forge --strict-channel-priority r-arrow conda conda-forge data wrangling https://arrow.apache.org/docs/r/ optional Note: This currently seems to work for Windows but struggles with installation on Linux! Arrow is required to save data frames as .feather files (which is the format to exchange data between python and R). This documented error happens on the server: https://arrow.apache.org/docs/r/articles/install.html#package-failed-to-build-c-dependencies R cross-platform
r-matrixstats conda install -c conda-forge r-matrixstats conda conda-forge data wrangling https://anaconda.org/conda-forge/r-matrixstats optional required for reproducing Xia et al. CCA analysis R
r-pma conda install -c conda-forge r-pma conda conda-forge statistical modelling https://anaconda.org/conda-forge/r-pma optional Package to conduct sparse canonical correlation analysis Why do I added this? This is the same as install.packages('PMA') that can also be found in this spreadsheet? Choose either this package or install PMA package with CRAN, but not both. If you can succesfully use the gemmr package and if you can rerun Xia et al. script, then you don't have to use install.package('PMA'') R
PMA install.packages('PMA') cran statistical modelling https://cran.r-project.org/web/packages/PMA/index.html optional required for reproducing Xia et al. CCA analysis R
lme4 install.packages('lme4') cran statistical modelling https://cran.r-project.org/web/packages/lme4/lme4.pdf optional Fitting mixed models in R Note, that when using the python package pymer4, you will already have lme4 installed, so this installation would become obsolete. You might also need to install stamod (https://community.rstudio.com/t/error-message-when-trying-to-install-lmer-package-and-load-lmer-library/85418) R
r-dendextend conda install -c conda-forge r-dendextend conda conda-forge plotting https://r-charts.com/part-whole/circular-dendrogram/ optional Allows to customize dendrograms (e.g. coloring branches, adding labels) Should be installed together with circlize R
r-circlize conda install -c conda-forge r-circlize conda conda-forge plotting https://r-charts.com/part-whole/circular-dendrogram/ optional Allows to draw circular dendrograms Should be installed together with dendextend R

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