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Extract, Analyze and Visualize Mutational Signatures with Sigminer

2 Package prerequisite and installation

2.1 Package prerequisite

All R package dependencies of sigminer can be checked at specific fields of DESCRIPTION file. Of note, unlike common R package, many key features of sigminer are only available when the suggested packages are installed. Most of them are from Bioconductor, so R package BiocManager must be installed before installing sigminer. You have to use BiocManager instead of install.packages() to install sigminer. If you want to handle other reference genome data except hg19, e.g., for hg38, you also have to install Bioconductor package BSgenome.Hsapiens.UCSC.hg38 before/after installing sigminer.

2.2 Package installation

The stable release version of sigminer package can be installed from the CRAN:

install.packages("BiocManager")
BiocManager::install("sigminer", dependencies = TRUE)

Set dependencies = TRUE is recommended because many packages are required for accessing full features provided by sigminer (we described this in previous section). The development version of sigminer package can be installed from Github or Gitee after installing CRAN version sigminer:

install.packages("remotes")
# From GitHub
remotes::install_github("ShixiangWang/sigminer", dependencies = TRUE)
# From Gitee
remotes::install_git("https://gitee.com/ShixiangWang/sigminer", dependencies = TRUE)

If you see notification of package update, please keep this package up to date.

The sigminer is also available in Conda forge channel. If you are using Conda, you can install sigminer with:

# Please note version number of the bioconda release

# You can install an individual environment firstly with
# conda create -n sigminer
# conda activate sigminer
conda install -c bioconda -c conda-forge r-sigminer

2.3 Package loading

To load package, run:

More info about sigminer can be given as:

hello()
## Thanks for using 'sigminer' package!
## =========================================================================
## Version: 2.1.1
## Run citation('sigminer') to see how to cite sigminer in publications.
## 
## Project home : https://github.com/ShixiangWang/sigminer
## Bug report   : https://github.com/ShixiangWang/sigminer/issues
## Documentation: https://shixiangwang.github.io/sigminer-book/
## =========================================================================
##

2.4 Package references

All datasets/functions are well organized and documented at package referrence list. For checking usage of a specific function fun, you can also run ?fun in your R console. For example, to see usage read_copynumber()

library(sigminer)
?read_copynumber