README.md

In lgatto/biocpkgs: Learning about Bioconductor packages

The biocpkgs package

The biocpkgspackage offers simple utilities to explore download data and dependencies of Bioconductor packages. See this vignette for a usecase.

Installation

library("devtools")
install_github("lgatto/biocpkgs")

Download statistics

library("biocpkgs")
dl <- pkg_download_data(c("MSnbase", "rpx"))
dl

## # A tibble: 132 x 6
##     Year Month Nb_of_distinct_IPs Nb_of_downloads package       Date
##    <int> <chr>              <int>           <int>   <chr>     <date>
##  1  2017   Jan                684            1209 MSnbase 2017-01-01
##  2  2017   Feb                660            1152 MSnbase 2017-02-01
##  3  2017   Mar                705            1452 MSnbase 2017-03-01
##  4  2017   Apr                697            1407 MSnbase 2017-04-01
##  5  2017   May               1087            2040 MSnbase 2017-05-01
##  6  2017   Jun               1058            2000 MSnbase 2017-06-01
##  7  2017   Jul                  0               0 MSnbase 2017-07-01
##  8  2017   Aug                  0               0 MSnbase 2017-08-01
##  9  2017   Sep                  0               0 MSnbase 2017-09-01
## 10  2017   Oct                  0               0 MSnbase 2017-10-01
## # ... with 122 more rows

library("ggplot2")
ggplot(dl, aes(x = Date, y = Nb_of_distinct_IPs,
                group = package, colour = package)) + geom_line()

Package dependencies

library("biocpkgs")
p <- c("MSnbase", "mzR") ## packages of interest
g <- pkg_dep_graph(pkgs = p) 
g

## A graphNEL graph with directed edges
## Number of Nodes = 30 
## Number of Edges = 50

plot_pkg_dep_graph(g, pkgs = p, fs = 25)

lgatto/biocpkgs documentation built on May 13, 2019, 1:38 a.m.