In RGLab/cytoinstaller: cyto package Installation from repositories, Including 'bioconductor' and 'GitHub'

This package is a lightweight wrapper of some functions in remotes. It installs the most recent version of cyto packages from the common public repositories e.g. Bioconductor, CRAN, as well as CYTO repository, which provides the cyto packages built by github actions triggered by pushed commits.

Installation

Install the released version of remotes from CRAN:

remotes::install_github("RGLab/cytoinstaller")

Usage

To install the latest version of a cyto package (and also install or update its dependencies.)

cytoinstaller::install_cyto("ggcyto")

To install/update all cyto packages

cytoinstaller::install_cyto()
#select bioc version manually
cytoinstaller::install_cyto(bioc_ver = "devel")

To get the package info from CYTO repo,

cytoinstaller::cyto_repo("ggcyto")

To list all the package info,

cytoinstaller::cyto_repo()

knitr::opts_chunk$set(echo = TRUE)

library(cytoinstaller)
library(kableExtra)
library(dplyr)
cyto_repos <- getOption("cyto_repos")
df <- do.call(rbind, lapply(cyto_repos, function(pkg){
                            data.frame(package = pkg
                                       , release = paste0("https://github.com/RGLab/", pkg, "/workflows/build/badge.svg?branch=release")
                                       , devel = paste0("https://github.com/RGLab/", pkg, "/workflows/build/badge.svg?branch=master")
                                       , link = paste0("https://github.com/RGLab/", pkg, "/actions") 
                                      )
                          })
            )
df1 <- df

CYTO repo build status

df[,1:3] %>% mutate(release := "", devel := "") %>% 
  kbl(booktabs = T) %>%
  kable_paper(full_width = F) %>%
  column_spec(1, link = df1$link)%>%
  column_spec(2, image = df1$release)%>%
  column_spec(3, image = df1$devel)

RGLab/cytoinstaller documentation built on Dec. 31, 2020, 4:21 p.m.