Chapter 5 Web Resource

5.1 Cellxgene VIP

cellxgene VIP source code: https://github.com/interactivereport/cellxgene_VIP
cellxgene VIP demo sites: https://cellxgenevip-ms.bxgenomics.com [Schirmer / Rowitch MS, Human brain snRNAseq 46k cells, Nature 2019 Schirmer et al]

cellxgene: https://github.com/chanzuckerberg/cellxgene
cellxgene tutorial: https://cellgeni.readthedocs.io/en/latest/visualisations.html
cellxgene features: https://chanzuckerberg.github.io/cellxgene/posts/gallery
cellxgene data preparation: https://chanzuckerberg.github.io/cellxgene/posts/prepare.html

scanpy: https://github.com/theislab/scanpy
scanpy plots: https://scanpy-tutorials.readthedocs.io/en/latest/visualizing-marker-genes.html
diffxpy: https://github.com/theislab/diffxpy
diffxpy tests: https://diffxpy.readthedocs.io/en/latest/tutorials.html#differential-testing

Benchmarking of interactive data visualization of single-cell RNAseq data — Batuhan Cakir : https://www.youtube.com/watch?v=3nH2xi_Ni6I
sceasy: convertor of scRNA-Seq data formats https://github.com/cellgeni/sceasy
jupytext: https://jupytext.readthedocs.io , Jupyter Notebooks as Markdown Documents, Julia, Python or R Scripts
nbconvert: https://nbconvert.readthedocs.io , Convert a Jupyter .ipynb notebook document file into another static format including HTML, LaTeX, PDF, Markdown, and more
R magic: https://rpy2.github.io/doc/latest/html/interactive.html#rmagic , Magic command interface for interactive work with R in ipython. %R and %%R are for the line mode where one line of R code will be executed, and the cell mode where a block of R code will run, respectively.