Useful Links

This page lists external resources that might be helpful. This page is connected to HackMD which is a markdown viewer. It is published as a HackMD Book so all the content on this page is public. View the HackMd Book version to look through the links more comfortably and to see this page in its correct layout.

• 

• ZAS

Utilitites

• Seatplan
• ZAS BinAC
• ProjectTemplate - by Denes
• ScWorkflow - by Denes
• Cookiecutter - project templates to clone
  • JupyterBook
  • ScVerse
• SaezLab Proj Template - scverse inspired
• Make R project Binder
• Graphics

Online Books

• Theis: sc-best-practices
• R for DataScience
• Advanced R
• R Packages 📦
• R Markdown Cookbook
• Efficient R Programming
• Hands-On Machine Learning with R
  • Random Forest Training
  • Slides to Hands-On Machine Learning with R
  • Website
• Interpretable Machine Learning
  • SHAP
  • Limitations of Interpretable Machine Learning Methods
• The caret Package
• An Introductino to Statistical Learning - Microbiome
• Practical Computing and Bioinformatics for Conservation and Evolutionary Genomics

To get into single cell analysis read through the OSCA book.

An Article a day…

• Datascientest

Events

• Mar 21 online reg: Data visualization EMBO Workshop
• E-Science-Tage March 2023
• NHR4CES Workshops

• Weekly or Monthly

  • ScVerse Meetings

• Workshops & Resources

  • Scientific Computing and Optimization Teaching
  • Bioconductor - 2022

Projects

• CRC 1550

Maths, ML, etc.

• distill
• StatisticalRethinking by Richard McElreath
  • R - PyMC3 port
  • Python - PyMC3 port

• Bayes

• "Bayesian Modeling and Computation in Python" by Osvaldo A. Martin, Ravin Kumar, Junpeng Lao
• "Bayesian Cognitive Modeling" by Michael Lee and EJ Wagenmakers
  • Pyton - PyMC3 port
• "Bayesian Statistical Methods" by Brian J. Reich and Sujit K. Ghosh
  • Python - PyMC3 port
• "Bayes Rules" by Alicia A. Johnson, Miles Q. Ott, and Mine Dogucu
  • Python - PyMC port
• Bayesian Data Analysis (and others by Gelman)
• Bayesian Neural Networks

• Deep Learning

  • Kipoi
    • Seminar Series

Bilingual

• RStudio - bilingual - examples of bilingual packages R & Python
  • rAndPython
• R in Python

R

• renv
• Bioconductor package overview

• Seurat & SCE

  • Essential Commands
  • SeuratDisk
  • Seurat - ObjectInteraction
  • Seurat AnnData Conversion
    • Convert
  • [SingleCellExperiment](https://bioconductor.org/packages/devel/bioc/vignettes/SingleCellExperiment/inst/doc/devel.html#1_Introduction
  • TidySummarizedExperimeint
• Package
• Dashboards
• Renv
  • Conda
• Conda
  • Using R in Conda
• RMarkdown Cookbook
• Mastering Shiny
• Libraries
  • scater
  • plyr - as.quoted
  • stats - quantile
  • dplyr

Python

• Python Data Science Handbook
• Params
• Jupyter Documentation
• Write to CSV Files
• Network Vis interactive

• GUIs

  • which-python-gui-library
  • qt-for-python
  • why qt/qml
  • Python Wiki

• Dashboards

  • JupyterNotebook with Dropdown
  • Panel - Pipelines
  • Panel_- Concurrency
  • Interact package
• Muon
• fnc
• benedict for dicts
• Multiprocessing
• Pathos
• FLIT put pckgs on PyPI
• ParsingCommandLineArguments
• ReadTheDocs - publish online tutorial

• JupyterBook

  • Shpinx-Design
    • Grids
  • MYST
    • Substitutions
    • Notebook
  • Page Layout/full width
  • TOC
  • Margin/Sidebar
  • R Notebook
  • API
    • API Documentation
    • Sphinx Autosummary
  • Build PDF
  • Hypothes - WebsiteAnnoations
  • Diagrams
    • Diagram Options
    • Mermaid - Diagrams
      • Syntax
      • Mermaid.live
    • Mermaid - Sphinx
    • PlantUML Syntax

• Packages & Envs

  • pipx: install/run py applications in isolated envs
    • how to set up a perfect python project
  • Poetry
  • pipfile-vs-setuppy

• VIS

  • JS+Jinja+Flask - getting data from your python program to JavaScript inside of a Jinja HTML template
  • Jinja - html templating engine
  • Voilà
  • Display Markdown from Code Cells
  • Interactive Tables

• Syntax etc.

  • all
  • init.py
  • globals()

Bash

• VIM
• sshfs - MacFuse

Julia

• Julia Random Variables

ATAC Analysis

• ArchR

Transcriptomics

• Quickomics - Shiny App for analysis

Single Cell Analysis

• Tutorial

• Best Practice Snakemake Workflow

• 2022 - SingleCellCourse

  • Github

• Workshop scRNAseq

  • Github

• Glossary of sc terms

• 2019 - scRNA-python-workshop

  • Github

• 2019 scWorkshop

• scDIOR SCFramework transformations

• List of Software Packages

• How does data structure impact cell-cell similarity? - Bray Curtis

• scAnnotatR - Celltype Prediction (2022)

• Theis

  • Over 1000 tools reveal trends in the single-cell RNA-seq analysis landscape
  • Theis Review 2019

• singleCellGermany

• scrna-tools.org

• Github- scRNA-seq_notes

• Pipelines

  • RNAlysis
  • Snakemake
  • Nextflow
  • Galaxy

• Paper

  • Transformation and Preprocessing

• OSCA (R)

  • OSCA - Analysis overview
  • OSCA - Getting scRNA-seq datasets
  • OSCA - Unfiltered human PBMCs (10X Genomics)
  • aggregateData

• Seurat (R)

  • Seurat Class
  • Seurat - Guided Clustering Tutorial
  • pbmc3k_tutorial
  • Regroup Idents
  • Azimuth - Annotation

• PathwayEnrichmentAnalysis

  • G:Profiler
  • On the influence of several factors on pathway enrichment analysis

• AnnData (Python)

  • scverse

• Other

  • Partek Flow

Spatial

• Minerva
• A Web-based Software Resource for Interactive Analysis of Multiplex Tissue Imaging Datasets

Saezlab

• LIANA
  • R Tutorial
  • LIANA-py
• Decoupler
  • python
  • paper
• ShinyFUNKI
• BioCypher
• PyPath
• OmniPath
• CellNOpt
  • Bioconductor
  • Github

Projects

• TSTIM
  • Seurat obj by Florian Wünnemann

Infrastructure

• FDM
  • Coscine
    • S3 storage used by RWTH
• Orcestra
  • Paper
• de.NBI – Cloud
  • HD Wiki
• BSC Support Knowledge Center - Usage of Modules
• bwHPC
  • Wiki BwForCluster BinAC
  • Courses
  • ZAS - Central Application Site
• ListServ UniHeidelberg
• HumanCellAtlas
• Github
  • Sourcegraph - search
• Fenix
• URZ
  • IT-Service
  • Archiving & Backup
  • heiArchive
    • heiArchive
• Databases
  • • Sherlock
      • SQL based, Github not really maintained anymore
  • SQLiteBrowser
  • Django vs. Flask
  • Jupyter Magics with SQL
  • Fugue - SQL+Python (+Spark/Dask/Ray) -Python+SQL+Jupyter Notebook
  • NoSQL one to one
  • ipython-sql
  • SQLCell (prob. not the best solution)
  • RealPython - Postgres
  • Psycopg - PostgreSQLAdapter
  • PostgreSQL
  • SQLAlchemy
  • SQLAlchemiy + MariaDB
  • Graph database
  • Zendro - DataWarehouse

Workflows

• WorkflowHub

Nextflow

• DolphinNext
  • scPipeline_LungCellAtlas
• Nextflow Training
• nf-core Creating Pipelines

Snakemake

• Robin's Snakemake Tutorial
• Installation
• On Cluster
• Rules
• ParamSpaceExploration

Conda

• Conda
• Basilisk - Conda with Python created from R
• Snakemake & Conda
• Remove Conda
• Channels
  • Bioconda

Container

• Singularity

  • Sign Container
  • Reproducibility
  • Build
  • Shell
  • Apps
• Snakemake & Container
  • Singularity
  • Tutorial Slides
  • Tutorial Data
• ml-jax

Sequencing Types

• HTSeq

Atlas

• DISCO - samples & integration
• Mapping data to HLCA
• HLCA Reproducibility

Web Development

• JsFiddle
• SVGPathBuilder
• BootstrapAnimationExamples
• LiveWeave
• SASS
  • Installation
  • To CSS
• CSS
  • Tree
  • HorizontalTree
  • CSSAnimation

Other

• How to make figures, presentations, …
• Paper from Arnau (Permedcoe)
• ReactomeGSA - Pathway Analysis
• Probabilistic latent variable models
• DFG-Projects
• Reformat HDD for Mac
• Nature Reporting Standards

Plots

• DataToViz

Paper

2021

• saez: A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
• #astrocytes #brain #microglia
• COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

2020

• #astrocytes #medulloblastoma

Questionnaires

• Typeform

RDM

• LPAM
  • Poster
  • CMMI
• E-Science Tage 2021
• Pandoc - a universal document converter
• BioDATEN
  • BioDATEN, HUBzero - Paper
• NFDI - Paper
• ReSUS
• Dataverse
  • DaRUS - Stuttgart
• AIMS
  • RDF
  • SHACL

Training

• From functional genomics to systems biology
• EMBL-EBI Training Account

Biology

• Look up terms

Presenting & Writing

• Tools for science
• Writer's block
• Storytelling in Powerpoint
• Rajlab - Improve presentaion
• Rajlab - Structure talk
• Rajlab - Figures
• David L Stern - HowTo give a talk