notes_cellxgene.md

Notes for installing cellxgene

cellxgene is an interactive browser for single-cell data that is being developed by the CZI.

• Tutorials for exploring data using cellxgene
• CZI's install help -- this only installs the basic cellxgene browser -- we typically prefer to install it along with the VIP tools that allow for violin plots and more
• collection of browsable public data sets

Pre-requisites on MacOS are:

• command line tools installed?

  • if NOT, run xcode-select --install in the Terminal

• conda installed?

  • if NOT, do that first; see https://docs.conda.io/projects/continuumio-conda/en/latest/user-guide/install/macos.html

  curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O Miniconda3-latest-MacOSX-x86_64.sh
  bash Miniconda3-latest-MacOSX-x86_64.sh
  ### AFTER YOU INSTALL CONDA, RESTART THE TERMINAL! ####
  

• R installed?

• if NOT, install R: download https://cran.r-project.org/bin/macosx/base/R-4.0.4.pkg and follow instructions

Then, let's brace yourself for cellxgene VIP:

## cellxgene  VIP install
git clone https://github.com/interactivereport/cellxgene_VIP.git
cd cellxgene_VIP
#conda config --set channel_priority flexible
conda env create -n VIP -f VIP.macOS.yml
conda activate VIP
./config.macOS.sh
export LIBARROW_MINIMAL=false
#  ensure that the right instance of R is used.
# e.g. system-wide: /bin/R or /usr/bin/R ;
# local R under conda: ~/.conda/envs/VIP_conda_R/bin/R
which R

## DO CAIRO BEFORE ALL ELSE 
conda install -c anaconda cairo 
conda install -c conda-forge cairo 

## INSTALL PACKAGES
conda install -c anaconda cairo 
conda install -c conda-forge cairo 
R -q -e 'if(!require(devtools)) install.packages("devtools",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(Cairo)) install.packages("Cairo",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(foreign)) install.packages("foreign",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(ggpubr)) install.packages("ggpubr",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(ggrastr)) install.packages("ggrastr",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(arrow)) install.packages("arrow",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(Seurat)) install.packages("Seurat",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(rmarkdown)) install.packages("rmarkdown",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(tidyverse)) install.packages("tidyverse",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(viridis)) install.packages("viridis",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(hexbin)) install.packages("hexbin",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(ggforce)) install.packages("ggforce",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(fastmatch)) install.packages("fastmatch",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(RcppRoll)) install.packages("RcppRoll",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(BiocManager)) install.packages("BiocManager",repos = "http://cran.us.r-project.org", type="binary")'
R -q -e 'if(!require(fgsea)) BiocManager::install("fgsea")'
R -q -e 'if(!require(rtracklayer)) BiocManager::install("rtracklayer")'

# These should be already installed as dependencies of above packages
R -q -e 'if(!require(dbplyr)) devtools::install_version("dbplyr",version="1.0.2",repos = "http://cran.us.r-project.org")'
R -q -e 'if(!require(RColorBrewer)) devtools::install_version("RColorBrewer",version="1.1-2",repos = "http://cran.us.r-project.org")'
R -q -e 'if(!require(glue)) devtools::install_version("glue",version="1.4.2",repos = "http://cran.us.r-project.org")'
R -q -e 'if(!require(gridExtra)) devtools::install_version("gridExtra",version="2.3",repos = "http://cran.us.r-project.org")'
R -q -e 'if(!require(ggrepel)) devtools::install_version("ggrepel",version="0.8.2",repos = "http://cran.us.r-project.org")'
R -q -e 'if(!require(MASS)) devtools::install_version("MASS",version="7.3-51.6",repos = "http://cran.us.r-project.org")'
R -q -e 'if(!require(data.table)) devtools::install_version("data.table",version="1.13.0",repos = "http://cran.us.r-project.org")'


###
# Run cellxgene on test file
cellxgene launch https://cellxgene-example-data.czi.technology/pbmc3k.h5ad


conda activate VIP
cellxgene launch our_data.h5ad

References for cellxgene

• Bioarxiv manuscript of cellxgene
• Documentation for cellxgene Desktop
• Bioarxiv manuscript of cellxgene VIP
• Documentation for cellxgene VIP