BrepPhylo

An R package with functions to perform phylogenetic reconstruction of B-cell receptor (BCR) lineages.

The BrepPhylo package contains a set of functions written for the purpose of performing lineage reconstruction of a large number of B cell clonotypes obtained via high-throughput sequencing of immunoglobulin repertoires. The aim is to provide 'wrappers' around popular, existing tools for lineage reconstruction, detect Class-Switch Recombination (CSR) events from lineage trees, and generate easy-to-interpret output to analyse these lineages.

Installation

MacOS / Linux

In R:

# install these dependencies on Bioconductor if you haven't had them installed already
install.packages('BiocManager')
BiocManager::install( c("Biostrings", "msa", "GenomicRanges", "GenomicAlignments") )

# install the package; the following install those dependent packages available on CRAN
require(devtools)
install_github("Fraternalilab/BrepPhylo", ref = "main", dependencies = TRUE)

To run the examples in the vignettes the dnapars program from the PHYLIP package is required. An executable of the program is shipped with the package; this works for Linux systems.

For MacOS please follow instructions from PHYLIP to download and install the program. You will need to supply the absolute filepath of the dnapars executable when you run some of the functions in BrepPhylo. See the vignettes (below) for details.

Windows

1. Make sure you have Rtools installed. Instructions can be found here. Basically:

• Run the installer. You can install the program anywhere you want.
• from R, run: writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
• Close and restart R. Verify this is set up by running this in R Sys.which("make"). It should return the path where Rtools is installed.

2. Install the devtools R package.

• In R: install.packages("devtools")

3. Next download PHYLIP from the link above. Make sure you selected the Windows pre-computed binaries.

• You will then download a zip file. Extract the zip file.
• The file dnapars.exe in the exe subfolder of the extracted directory is the filepath you need to supply when running certain functions in BrepPhylo. See the vignettes (below) for details.

4. BrepPhylo calls the alakazam R package in running PHYLIP. As of 30th June 2021, you need to download the development version of the alakazam package rather than the standard avaialble pre-compiled version (only for Windows; the CRAN available version works as expected for MacOS/Linux machines).

• In R: devtools::install_bitbucket("kleinstein/alakazam")

5. (Optional) If you wish to generate alignment PDF files for sequences, you need a working copy of LaTex. Check out distributions such as MiKTeX or TeX Live and install them. Note: this is an optional step, you can indicate not to generate such output when running BrepPhylo functions, lineage trees will still be reconstructed and you can still use other functionalities in the package as designed.
6. Now follow the instructions above for MacOS/Linux to install BrepPhylo.

We have tested running the vignette on Windows machines and it works as expected.

Examples

Vignettes in HTML and PDF formats are provided here.

Contact

Joseph Ng (@josef0731). For issues with this package please open an issue in this github repository.

Acknowledgement

To members of the Dunn-Walters lab, University of Surrey for developing ideas to implement in the package, and to Christian Margreitter (@CMargreitter) for building the initial version of the package.