BITE

BITE: BioInformatics Tools for Everyone

Nowadays, molecular data analyses for biodiversity studies often require advanced bioinformatics skills, preventing many life scientists from analysing their own data autonomously. BITE R package provides complete and user-friendly functions to handle SNP data and third-party software results (i.e. Admixture, TreeMix), facilitating their visualization, interpretation and use. Furthermore, BITE implements additional useful procedures, such as representative sampling and bootstrap for TreeMix, filling the gap in existing biodiversity data analysis tools.

Examples of BITE function outputs from human trial datasets. A) Membership coefficients estimated with Admixture software at K= 2, 3, 4, 7 and plotted in curcular fasihion with the membercoef.circos function of BITE; B) Gene flow analysis using TreeMix. Nodes robustness was estimated with 100 bootstrap replicates and plotted using the treemix.bootstrap function of BITE. Fig1_20190924

The BITE manuscript is available at bioxriv.org. Link to paper & doi

Instructions

The package could be installed from source in R. The necessary dependencies are below reported.

Faster method (using devtools)

# install devtools
install.packages("devtools")

# install BiocManager (if necessary)
if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

# install SNPRelate using BiocManager
BiocManager::install("SNPRelate")

# load devtools
library(devtools)

# install BITE V2 from source
devtools::install_local("BITEV2_2.1.0.tar.gz")

Dependencies

SNPRelate >= 1.32.2
ggplot2 >= 3.4.2
gridExtra >= 2.3
stringr >= 1.5.0
shiny >= 1.7.4.1
dplyr >= 1.1.2
plotly >= 4.10.2
ggrepel >= 0.9.3
data.table >= 1.14.8
RCircos >= 1.2.2
OptM >= 0.1.6
poolfstat >= 2.1.2
RColorBrewer >= 1.1-3

How to cite

Milanesi M., Litta P., Vajana E., Somenzi E., Bomba L., Pietrucci D., Ajmone-Marsan P., Chillemi G., Capomaccio S., Colli L., 2017. BITE: an R package for biodiversity analyses. bioRxiv 181610. doi:10.1101/181610

Maintainers contacts

Marco Milanesi marco.milanesi.mm@gmail.com
Paolo Litta paolo.litta.pl@gmail.com
Stefano Capomaccio capemaster@gmail.com
Elia Vajana vajana.elia@gmail.com
Lorenzo Bomba lory.bomb@gmail.com