cgmisc is a R package that enables enhanced data analysis and visualisation of results from GWAS. The package contains several utilities and modules that complement and enhance the functionality of existing softwares. It also provides several tools for advanced visualisation of genomic data and utilises the power of the R language to aid in preparation of publication-quality figures. Some of the package functions are specific for the domestic dog (Canis familiaris) data.
Beginning from version 2.9.11, we are no longer using releases system. Instead, we maintain cgmisc in the CD/CI manner. From time to time, major versions will be frozen and available as source packages. Otherwise, track commit messages to know what has changed.
For you who are familiar with Docker, there is a
cgmisc container available from the DockerHub, so that you can just:
docker pull quiestrho/cgmisc:latest
cgmisc enchances functionalities of
GenABEL package which is, unfortunately, no longer supported. Thus you will need to install it manualy from source available on CRAN Package Archives:
install.packages("https://cran.r-project.org/src/contrib/Archive/GenABEL.data/GenABEL.data_1.0.0.tar.gz", type='source', repos=NULL)
install.packages("https://cran.r-project.org/src/contrib/Archive/GenABEL/GenABEL_1.8-0.tar.gz", type='source', repos=NULL)
In addition, some more packages are required, but they should be installed automatically.
We recommend to use an excellent
renv package to recreate optimal environment for
cgmisc installation. First, retrieve the
and put it in your project directory. Next, type this in R:
install.packages(renv) library(renv) renv::init()
Otherwise, we recommend installing cgmisc by using:
To install using the tarball, open a terminal and type:
R CMD INSTALL cgmisc_[version].tar.gz
How to cite
Kierczak M, Jablonska J, Forsberg SKG, Bianchi M, Tengvall K, Pettersson M, Scholz V, Meadows JRS, Jern P, Carlborg O Lindblad-Toh K. cgmisc: enhanced genome-wide association analyses and visualization. Bioinformatics. Oxford University Press; 2015;31: 3830-3831. doi:10.1093/bioinformatics/btv426
Selected publications that used
Here we list some publications where cgmisc has been helpful: