# Useful Links
- <a href="http://­www.schulhomepage.de/" ­target="_blank"­>Schulhomepage.de</a>
- [Useful Information Snippets](https://hackmd.io/@Thalla/SJdprH3qc)
- [](https://hackmd.io/vEJkZimbQty5Eu6rGTFI-w)
- [Miro](http://miro.com/app/board/o9J_li3o4nQ=/?share_link_id=217108224925)

## Utilitites
- **[ProjectTemplate](http://github.com/saezlab/python-project)** - by Denes
- **[ScWorkflow](http://github.com/saezlab/scworkflow)** - by Denes
- [Cookiecutter](http://github.com/cookiecutter/cookiecutter/tree/1.7.2) - project templates to clone
- **[JupyterBook](http://github.com/executablebooks/cookiecutter-jupyter-book)**
- [ScVerse](http://github.com/scverse/cookiecutter-scverse)
- **[SaezLab Proj Template](http://github.com/saezlab/python-project)** - scverse inspired
- [Make R project Binder](http://github.com/karthik/holepunch)
- [Graphics](http://github.com/saezlab/graphics)

## An Article a day...
- [Datascientest](https://datascientest.com/de/category/python-de)

## Ucoming Events
- [E-Science-Tage](http://e-science-tage.de/de/anmeldung)

## Projects
- [CRC 1550](https://www.crc1550.com/project-inf)

## Maths, ML, etc.

- [distill](https://distill.pub/)
- [StatisticalRethinking by Richard McElreath](https://xcelab.net/rm/statistical-rethinking/)
- [R](http://github.com/pymc-devs/resources/tree/main/Rethinking) - PyMC3 port
- [Python](http://github.com/pymc-devs/resources/tree/main/Rethinking_2) - PyMC3 port
- ### Bayes
- ["Bayesian Modeling and Computation in Python" by Osvaldo A. Martin, Ravin Kumar, Junpeng Lao](https://bayesiancomputationbook.com/welcome.html)
- ["Bayesian Cognitive Modeling" by Michael Lee and EJ Wagenmakers](https://bayesmodels.com/)
- [Pyton](http://github.com/pymc-devs/resources/tree/main/BCM) - PyMC3 port
- ["Bayesian Statistical Methods" by Brian J. Reich and Sujit K. Ghosh](https://bayessm.wordpress.ncsu.edu/)
- [Python](http://github.com/pymc-devs/resources/tree/main/BSM) - PyMC3 port
- ["Bayes Rules" by Alicia A. Johnson, Miles Q. Ott, and Mine Dogucu](https://www.bayesrulesbook.com/index.html)
- [Python](http://github.com/pymc-devs/resources/tree/main/Bayes_Rules) - PyMC port
- [Bayesian Data Analysis (and others by Gelman)](https://stat.columbia.edu/~gelman/books/)
- [Bayesian Neural Networks](https://www.cs.toronto.edu/~duvenaud/distill_bayes_net/public/)
- ### Deep Learning
- [Kipoi](https://kipoi.org/)
- [Seminar Series](https://kipoi.org/seminar/)

## Bilingual
- [RStudio - bilingual](https://www.rstudio.com/blog/creating-collaborative-bilingual-teams/#.Yz8oDandv9I.twitter) - examples of bilingual packages R & Python
- [rAndPython](https://www.rstudio.com/solutions/r-and-python/)
## R
- [Bioconductor package overview](https://www.stephaniehicks.com/software/)
- [SeuratDisk](https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html) - Seurat AnnData Conversion
- [Convert](https://mojaveazure.github.io/seurat-disk/reference/Convert.html)
- [Package](https://tinyheero.github.io/jekyll/update/2015/07/26/making-your-first-R-package.html)
- [Dashboards](https://bookdown.org/yihui/rmarkdown/dashboards.html)
- [Renv](https://www.rstudio.com/blog/renv-project-environments-for-r/)
- [Conda](https://anaconda.org/conda-forge/r-renv)
- [Conda](https://docs.anaconda.com/anaconda/user-guide/tasks/using-r-language/)
- [Using R in Conda](https://www.biostars.org/p/450316/)
- [Seurat - ObjectInteraction](https://satijalab.org/seurat/articles/essential_commands.html#seurat-object-interaction-1)
- [SingleCellExperiment](https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/devel.html#1_Introduction
- [TidySummarizedExperimeint](https://www.bioconductor.org/packages/devel/bioc/vignettes/tidySummarizedExperiment/inst/doc/introduction.html)
- [RMarkdown Cookbook](https://bookdown.org/yihui/rmarkdown-cookbook/)
- [Mastering Shiny](https://mastering-shiny.org/index.html)
- *Libraries*
- [scater](https://bioconductor.org/packages/devel/bioc/manuals/scater/man/scater.pdf)
- [plyr - as.quoted](https://www.rdocumentation.org/packages/plyr/versions/1.8.7/topics/as.quoted)
- [stats - quantile](https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/quantile)

## Python
- [Python Data Science Handbook](https://jakevdp.github.io/PythonDataScienceHandbook/)
- [Params](https://param.holoviz.org/user_guide/Serialization_and_Persistence.html#serializing-with-json)
- [Jupyter Documentation](https://docs.jupyter.org/en/latest/use/use-cases/content-user.html)
- [Write to CSV Files](https://www.pythontutorial.net/python-basics/python-write-csv-file/)
- [Network Vis interactive](https://towardsdatascience.com/python-interactive-network-visualization-using-networkx-plotly-and-dash-e44749161ed7)
- ### Dashboards
- [JupyterNotebook with Dropdown](https://towardsdatascience.com/interactive-data-analysis-with-dropdown-menu-ipywidgets-and-plotly-in-jupyter-notebook-591a84a81b22)
- [Panel - Pipelines](https://panel.holoviz.org/user_guide/Pipelines.html)
- [Panel_- Concurrency](https://panel.holoviz.org/user_guide/Async_and_Concurrency.html)
- [Interact package](https://ipywidgets.readthedocs.io/en/latest/examples/Using%20Interact.html)
- [Muon](https://www.singlecell.de/index.php/resources/software/)
- [fnc](https://github.com/dgilland/fnc)
- [benedict](https://github.com/fabiocaccamo/python-benedict#find) for dicts
- [Multiprocessing](https://docs.python.org/3/library/multiprocessing.html)
- [Pathos](https://pathos.readthedocs.io/en/latest/pathos.html#module-pathos.threading)
- [FLIT](https://flit.pypa.io/en/stable/) put pckgs on PyPI
- [ParsingCommandLineArguments](https://stackoverflow.com/questions/3433603/parsing-command-line-arguments-in-r-scripts)
- [ReadTheDocs](https://docs.readthedocs.io/en/stable/tutorial/) - publish online tutorial
- ## JupyterBook
- [Shpinx-Design](https://sphinx-design.readthedocs.io/en/latest/index.html)
- [Grids](https://sphinx-design.readthedocs.io/en/latest/grids.html)
- MYST
- [Substitutions](https://myst-parser.readthedocs.io/en/latest/syntax/optional.html)
- [Notebook](https://myst-nb.readthedocs.io/en/v0.12.3/use/markdown.html)
- [Page Layout/full width](https://jupyterbook.org/en/stable/content/layout.html)
- [TOC](https://jupyterbook.org/en/stable/structure/configure.html?highlight=content#add-a-table-of-contents-to-a-pages-content)
- [Margin/Sidebar](https://jupyterbook.org/en/stable/content/layout.html)
- [R Notebook](https://jupyterbook.org/en/stable/file-types/jupytext.html?highlight=r%20notebook#custom-notebook-formats-and-jupytext)
- API
- [API Documentation](https://jupyterbook.org/en/stable/advanced/developers.html)
- [Sphinx Autosummary](https://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html)
- [Build PDF](https://jupyterbook.org/en/stable/advanced/pdf.html)
- [Hypothes](https://web.hypothes.is/) - WebsiteAnnoations
- Diagrams
- [Diagram Options](https://opencomputinglab.github.io/SubjectMatterNotebooks/diagram/sphinx-diagrammers.html)
- [Mermaid](https://mermaid-js.github.io/mermaid/#/integrations) - Diagrams
- [Mermaid - Sphinx](https://github.com/mgaitan/sphinxcontrib-mermaid)

- ## VIS
- [JS+Jinja+Flask](https://medium.com/@crawftv/javascript-jinja-flask-b0ebfdb406b3) - getting data from your python program to JavaScript inside of a Jinja HTML template
- [Jinja](https://jinja.palletsprojects.com/en/3.1.x/) - html templating engine
- [Voilà](https://voila.readthedocs.io/en/stable/index.html)
- [Display Markdown from Code Cells](https://colab.research.google.com/drive/1BosNRylNv8h4kzT4iexix3hiudVvqhhs?usp=sharing)
- [Interactive Tables](https://mwouts.github.io/itables/advanced_parameters.html)

## Bash
- [VIM](https://danielmiessler.com/study/vim/#changing)

## Julia
- [Julia Random Variables](https://azev77.github.io/posts/2021/04/blog-post-2/)
-
## ATAC Analysis

- [ArchR](https://www.archrproject.com/bookdown/creating-an-archrproject-1.html)

## Transcriptomics
- [Quickomics](https://academic.oup.com/bioinformatics/article/37/20/3670/6254183?login=true) - Shiny App for analysis

## Single Cell Analysis
- [How does data structure impact cell-cell similarity?](https://www.biorxiv.org/content/10.1101/2022.04.21.489121v1.full) - Bray Curtis
- [scAnnotatR - Celltype Prediction (2022)](https://www.bioconductor.org/packages/release/bioc/html/scAnnotatR.html)
- [Theis Review 2019](https://www.embopress.org/doi/full/10.15252/msb.20188746)
- [singleCellGermany](https://www.singlecell.de/index.php/resources/software/)
- [scrna-tools.org](https://www.scrna-tools.org/)
- [Github- scRNA-seq_notes](http://github.com/mdozmorov/scRNA-seq_notes)
- ### Paper
- [Transformation and Preprocessing](https://www.biorxiv.org/content/10.1101/2021.06.24.449781v2)
- ### OSCA \(R\)
- [OSCA - Analysis overview](https://bioconductor.org/books/3.14/OSCA.intro/analysis-overview.html#outline)
- [OSCA - Getting scRNA-seq datasets](https://bioconductor.org/books/3.14/OSCA.intro/getting-scrna-seq-datasets.html)
- [OSCA - Unfiltered human PBMCs (10X Genomics)](https://bioconductor.org/books/3.14/OSCA.workflows/unfiltered-human-pbmcs-10x-genomics.html)
- [aggregateData](https://rdrr.io/github/HelenaLC/ddSingleCell/man/aggregateData.html)
- ### Seurat \(R\)
- [Seurat Class](https://mojaveazure.github.io/seurat-object/reference/Seurat-class.html)
- [Seurat - Guided Clustering Tutorial](https://www.satijalab.org/seurat/articles/pbmc3k_tutorial.html)
- [pbmc3k_tutorial](https://satijalab.org/seurat/articles/pbmc3k_tutorial.html)
- [Regroup Idents](https://rdrr.io/github/satijalab/seurat/man/RegroupIdents.html)
- [Azimuth - Annotation](https://satijalab.github.io/azimuth/articles/run_azimuth_tutorial.html)
- [PathwayEnrichmentAnalysis](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010348#pcbi.1010348.s003)
- [G:Profiler](https://biit.cs.ut.ee/gprofiler/page/docs#significance_threhshold)
- [On the influence of several factors on pathway enrichment analysis](https://academic.oup.com/bib/article/23/3/bbac143/6572658#355039011)

- ### AnnData (Python)
- [scverse](https://scverse.org/)

- ### Other
- [Partek Flow](https://cbiit.webex.com/recordingservice/sites/cbiit/recording/f392c2b0b8e9103ab7bd005056810ea3/playback)

## Spatial
- [Minerva](https://vcg.seas.harvard.edu/publications/minerva-a-light-weight-narrative-image-browser)
- [A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets](https://www.biorxiv.org/content/10.1101/2022.08.18.504436v1.abstract)

## Saezlab
- LIANA
- [Tutorial](https://saezlab.github.io/liana/articles/liana_tutorial.html)
- Decoupler
- [python](https://decoupler-py.readthedocs.io/en/latest/api.html)
- [paper](https://academic.oup.com/bioinformaticsadvances/article/2/1/vbac016/6544613?login=false)
- [ShinyFUNKI](http://saezlab.github.io/ShinyFUNKI/)
- [BioCypher](http://github.com/saezlab/BioCypher)
- [PyPath](http://github.com/saezlab/pypath)
- [OmniPath](https://omnipathdb.org/#fig-design)
- CellNOpt
- [Bioconductor](https://www.bioconductor.org/packages/release/bioc/html/CellNOptR.html)
- [Github](http://github.com/saezlab/CellNOptR)

## Infrastructure
- [de.NBI – Cloud](https://www.denbi.de/cloud)
- [HD Wiki](https://cloud.denbi.de/wiki/Compute_Center/Heidelberg/#create-volumes)
- [BSC Support Knowledge Center - Usage of Modules](https://www.bsc.es/supportkc/docs/CTE-AMD/environment#modules-tool-usage)
- [bwHPC Wiki BwForCluster BinAC](https://wiki.bwhpc.de/e/BwForCluster_BinAC_Support)
- [HumanCellAtlas](https://data.humancellatlas.org/)
- [Github](https://docs.github.com/en/packages/working-with-a-github-packages-registry/working-with-the-container-registry)
- [Sourcegraph](https://sourcegraph.com/search?q=context:global+repo:%5Egithub.com/saezlab/&patternType=standard) - search
- [Fenix](https://fenix-ri.eu/access)
- [URZ](https://www.urz.uni-heidelberg.de/de)
- [IT-Service](https://it-service.uni-heidelberg.de/)
- [Archiving & Backup](https://www.urz.uni-heidelberg.de/de/service-katalog/speicher)
- [heiArchive](https://ui.heiarchive.uni-heidelberg.de/)
- [heiArchive](https://heibox.uni-heidelberg.de/f/be614887ca9a413e848f/)
- Databases
- [SQLiteBrowser](https://sqlitebrowser.org/)
- [Django vs. Flask](https://www.sitepoint.com/premium/books/python-web-development-with-django-and-flask-getting-started/read/1/k5d9vi8g/)
- [Jupyter Magics with SQL](https://towardsdatascience.com/jupyter-magics-with-sql-921370099589)
- [Fugue](http://github.com/fugue-project/fugue) - SQL+Python (+Spark/Dask/Ray)
-[Python+SQL+Jupyter Notebook](https://towardsdatascience.com/interoperable-python-and-sql-in-jupyter-notebooks-86245e711352)
- [NoSQL one to one](https://www.techighness.com/post/nosql-example-separate-collections-one-to-one-relationship-specialization-generalization/)
- [ipython-sql](https://github.com/catherinedevlin/ipython-sql)
- [SQLCell](https://tmthyjames.github.io/2019/may/SQLCell-version-2/) (prob. not the best solution)
- [RealPython - Postgres](https://realpython.com/search?q=postgres)
- [Psycopg - PostgreSQLAdapter](https://www.psycopg.org/)
- [PostgreSQL](https://wiki.ubuntuusers.de/PostgreSQL/)
- [SQLAlchemy](https://www.sqlalchemy.org/)
- [SQLAlchemiy + MariaDB](https://mariadb.com/de/resources/blog/using-sqlalchemy-with-mariadb-connector-python-part-2/)
- [Graph database](https://de.wikipedia.org/wiki/Graphdatenbank)

## Nextflow
- [DolphinNext](https://dolphinnext.readthedocs.io/en/latest/dolphinNext/overview.html)
- [scPipeline_LungCellAtlas](https://github.com/LungCellAtlas/scRNAseq_pipelines)
- [Nextflow Training](https://training.seqera.io/)
- [nf-core Creating Pipelines](https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core)

## Snakemake
- [Robin's Snakemake Tutorial](https://snakemake-workshop.readthedocs.io/en/latest/index.html#)
- [Installation](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html)
- [On Cluster](https://blobtoolkit.genomehubs.org/pipeline/pipeline-tutorials/running-the-pipeline-on-a-cluster/)
- [Rules](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html)
- [ParamSpaceExploration](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#parameter-space-exploration)

## Conda
- [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
- [Basilisk - Conda with Python created from R](http://www.bioconductor.org/packages/release/bioc/html/basilisk.html)
- [Snakemake & Conda](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#using-already-existing-named-conda-environments)
- [Remove Conda](https://askubuntu.com/questions/1301622/problem-in-removing-a-conda-created-environment)
- Channels
- [Bioconda](https://bioconda.github.io/tutorials/gcb2020.html#conda-channels)

## Container
- ### Singularity
- [Sign Container](https://docs.sylabs.io/guides/3.0/user-guide/signNverify.html)
- [Reproducibility](https://reproducibility.sschmeier.com/container/index.html)
- [Build](https://docs.sylabs.io/guides/3.0/user-guide/build_a_container.html#:~:text=build%20is%20the%20%E2%80%9CSwiss%20army,the%20formats%20supported%20by%20Singularity.)
- [Shell](https://docs.sylabs.io/guides/3.1/user-guide/cli/singularity_shell.html)
- [Apps](https://docs.sylabs.io/guides/3.1/user-guide/cli/singularity_apps.html)
- [Snakemake & Container](https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#containerization-of-conda-based-workflows)
- [Singularity](https://www.embl.org/groups/bioinformatics-rome/blog/2022/05/snakemake-profile-6-using-singularity-containers/)
- [Tutorial Slides](https://siscourses.ethz.ch/container_pipeline_tutorial/2_container_pipeline_tutorial.pdf)
- [Tutorial Data](https://sissource.ethz.ch/sispub/container_pipeline_tutorials/-/tree/master/ex01)
- [ml-jax](http://github.com/saezlab/permedcoe/tree/master/containers/ml-jax)

## Sequencing Types
- [HTSeq](https://github.com/htseq/htseq)

## Atlas
- [DISCO - samples & integration](https://www.immunesinglecell.org/repository)
- [Mapping data to HLCA](https://github.com/LungCellAtlas/mapping_data_to_the_HLCA)
- [HLCA Reproducibility](https://github.com/LungCellAtlas/HLCA_reproducibility/blob/main/notebooks/2_modeling_of_covariates_and_GWAS_analysis/1_variance_contribution_of_tech_and_bio_covariates.ipynb)

## Web Development
- [JsFiddle](http://jsfiddle.net/energee/UL9k9/)
- [SVGPathBuilder](https://codepen.io/anthonydugois/pen/mewdyZ)
- [BootstrapAnimationExamples](https://uicookies.com/bootstrap-animation/)
- [CSSAnimation](https://www.w3schools.com/css/tryit.asp?filename=trycss3_animation1)
- [LiveWeave](https://liveweave.com/)
-

## Other
- [How to make figures, presentations, ...](https://docs.google.com/document/d/1jBGk-u5auVCvI5EMaQnptMWbxHHl3ncIhKgIgEzjylw/edit)
- [Paper from Arnau (Permedcoe)](https://www.frontiersin.org/articles/10.3389/fmolb.2022.836794/full)
- [ReactomeGSA - Pathway Analysis](https://www.ebi.ac.uk/training/events/guide-multi-omics-pathway-analysis/)
- [Probabilistic latent variable models](https://mlo-lab.github.io/project/lvmodels/)
- [DFG-Projects](https://gepris.dfg.de/gepris/OCTOPUS)
- [Reformat HDD for Mac](https://www.youtube.com/watch?v=m4Em2mFZtk0)

## Plots

- [DataToViz](https://www.data-to-viz.com/)

## Paper
### 2021
- [#astrocytes #brain #microglia](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8697466/)
### 2020
- [#astrocytes #medulloblastoma](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337293/)

# Questionnaires

- [Typeform](https://www.typeform.com/explore/?utm_campaign=MiwmcAJH&utm_source=typeform.com-20373642-business&utm_medium=typeform&utm_content=typeform-endscreenbutton&utm_term=EN)

## RDM
- [LPAM](https://books.ub.uni-heidelberg.de/heibooks/reader/download/979/979-4-98021-1-10-20220413.pdf)
- [Poster](https://archiv.ub.uni-heidelberg.de/volltextserver/29719/13/Transparently_safeguarding_E-Science-Tage_2021.pdf)
- [CMMI](https://de.wikipedia.org/wiki/Capability_Maturity_Model_Integration#Zielorientierung_und_falsche_Verwendung_von_CMMI)
- [E-Science Tage 2021](https://books.ub.uni-heidelberg.de/heibooks/catalog/book/979)
- [Pandoc](https://pandoc.org/demos.html) - a universal document converter
- [BioDATEN](https://portal.biodaten.info/)
- [BioDATEN, HUBzero](https://books.ub.uni-heidelberg.de/heibooks/reader/download/979/979-4-98013-1-10-20220413.pdf) - Paper
- [NFDI](https://books.ub.uni-heidelberg.de/heibooks/reader/download/979/979-4-98016-1-10-20220413.pdf) - Paper
- [ReSUS](https://books.ub.uni-heidelberg.de/heibooks/reader/download/979/979-4-98001-1-10-20220413.pdf)
- Dataverse
- [DaRUS - Stuttgart](https://darus.uni-stuttgart.de/dataverse/darus)
- AIMS
- [RDF](https://www.w3.org/TR/1999/REC-rdf-syntax-19990222/)
- [SHACL](https://www.w3.org/TR/shacl/)

## Training
- [From functional genomics to systems biology](https://www.embl.org/about/info/course-and-conference-office/events/omx22-01/?utm_source=EMBL+courses+and+conferences&utm_campaign=52acb2d2a7-Quarterly_Newsletter_September2022&utm_medium=email&utm_term=0_b9f46bb4da-52acb2d2a7-91080865)
- [EMBL-EBI Training Account](https://www.embl.org/about/info/course-and-conference-office/2022/09/embl-ebi-training-logins/?utm_source=EMBL+courses+and+conferences&utm_campaign=52acb2d2a7-Quarterly_Newsletter_September2022&utm_medium=email&utm_term=0_b9f46bb4da-52acb2d2a7-91080865)

## Biology

- [Look up terms](https://www.biologyonline.com/)

## Past Events
- [Bioconductor - 2022](https://eurobioc2022.bioconductor.org/schedule/)