SplicingLore: a web resource for studying the regulation of cassette exons by human splicing factors

2023-06-30

Helene Polveche, Jessica Valat, Nicolas Fontrodona, Audrey Lapendry, Stephane Janczarski, Franck Mortreux, Didier Auboeuf, Cyril F Bourgeois

doi: https://doi.org/10.1101/2023.06.30.547181

https://splicinglore.ens-lyon.fr

Installation

Debian

sudo apt install libcurl4-openssl-dev libxml2-dev libssl-dev pandoc libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev librsvg2-dev libpq-dev  libudunits2-dev unixodbc-dev libproj-dev libgdal-dev libcairo2-dev libxt-dev 

sudo apt install build-essential zlib1g-dev libncurses5-dev libgdbm-dev libnss3-dev libreadline-dev libffi-dev libsqlite3-dev libbz2-dev

sudo apt install bedtools

R packages ( 4.2 )

install.packages("tidyverse", lib = "/usr/local/lib/R/site-library", dependencies = T) 
install.packages("plotly", lib = "/usr/local/lib/R/site-library", dependencies = T) 
install.packages("htmlwidgets", lib = "/usr/local/lib/R/site-library", dependencies = T) 

 if (!requireNamespace("BiocManager", quietly = TRUE))
   install.packages("BiocManager", lib = "/usr/local/lib/R/site-library", dependencies=T)
 BiocManager::install("rtracklayer", lib = "/usr/local/lib/R/site-library", dependencies=T)
 BiocManager::install("liftOver", lib = "/usr/local/lib/R/site-library", dependencies=T)

Python ( 3.10 )

pip3.10 install numpy panda loguru
pip3.10 install lazyparser statsmodels rich pymysql