In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

From: https://saezlab.github.io/liana/articles/liana_devel.html

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

if (!requireNamespace("remotes", quietly = TRUE))
install.packages("remotes")

remotes::install_github("cysouw/qlcMatrix")
remotes::install_github("nghiavtr/BPSC")
remotes::install_github("statOmics/zingeR")

Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS = TRUE) # ignore warningfrom iTALK 
BiocManager::install("ComplexHeatmap") # required forConnectome
# devtools::install_github('saezlab/OmnipathR\@ff3ad88e3915747e1b557bf44ac5396f9525dd7e')
devtools::install_github('saezlab/OmnipathR',dependencies = T)
# install 4.0 version of OmnipathR

# install tools

devtools::install_github("sqjin/CellChat",dependencies = T)
devtools::install_github('msraredon/Connectome', ref = 'master',dependencies = T)
devtools::install_github("Coolgenome/iTALK", build_vignettes = FALSE,dependencies = T) #A modified version of SingleCellSignalR (SCA) that enables external resources 
devtools::install_github(repo = "saezlab/SingleCellSignalR_v1",dependencies = T, subdir = "SingleCellSignalR")

# Finally, install LIANA

devtools::install_github('saezlab/liana')

Download yml file: https://github.com/saezlab/liana/blob/master/liana_env.yml

```{sh, engine.opts='-l'}

setup conda on bash

wget https://github.com/saezlab/liana/blob/master/liana_env.yml conda create -n liana_env conda activate liana_env conda install -c anaconda python=3.8.5 pip install squidpy wget https://github.com/saezlab/liana/blob/master/liana_env.yml conda env create -f liana_env.yml ```

C3BI-pasteur-fr/UTechSCB-SCHNAPPs documentation built on Jan. 12, 2025, 1:16 p.m.