Citations¶
Below is a list of the key software programs used in the main Brioche and Additional_functions scripts:
magrittr v2.0.4 Bache, S. M., Wickham, H., Henry, L., & Henry, M. L. (2022). Package ‘magrittr.’ R. Package Version.
Picard v3.2.0 Broad Institute. (2019). Picard toolkit. In Broad Institute, GitHub repository [Computer software]. https://broadinstitute.github.io/picard/
Blast v2.16.0 Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10(1), 421. https://doi.org/10.1186/1471-2105-10-421
bcftools v1.22 Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., & Davies, R. M. (2021). Twelve years of SAMtools and BCFtools. Gigascience, 10(2), giab008.
Nextflow v24.10.2 Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319. https://doi.org/10.1038/nbt.3820
stringi v1.8.7 Gagolewski, M. (2022). stringi: Fast and Portable Character String Processing in R. Journal of Statistical Software, 103(2), 1–59. https://doi.org/10.18637/jss.v103.i02
entrez-direct v22.4 Kans, J. (2024). Entrez direct: E-utilities on the UNIX command line. In Entrez programming utilities help [Internet]. National Center for Biotechnology Information (US).
Samtools v1.20 Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., & Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England), 25(16), 2078–2079. https://doi.org/10.1093/bioinformatics/btp352
bedtools v2.31.1 Quinlan, A. R., & Hall, I. M. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841–842.
R v4.4.1 R Core Team. (2024). R: A Language and Environment for Statistical Computing [Computer software]. R Foundation for Statistical Computing. https://www.R-project.org
ggplot2 v4.0.1 Wickham, H. (2011). ggplot2. WIREs Computational Statistics, 3(2), 180–185. https://doi.org/10.1002/wics.147
tidyverse v2.0.0 Wickham, H., Averick, M., Bryan, J., Chang, W., McGowan, L., François, R., Grolemund, G., Hayes, A., Henry, L., Hester, J., Kuhn, M., Pedersen, T. L., Miller, E., Bache, S. M., Müller, K., Ooms, J., Robinson, D., Seidel, D. P., Spinu, V., … Woo, K. (2019). Welcome to the Tidyverse. Journal of Open Source Software, 4(43), 1686. https://doi.org/10.21105/joss.01686
dplyr v1.1.4 Wickham, H., Francois, R., Henry, L., Muller, K., & Vaughan, D. (2025). dplyr: A Grammar of Data Manipulation [Computer software]. https://doi.org/10.32614/CRAN.package.dplyr
dbplyr v2.5.1 Wickham, H., Girlich, M., & Ruiz, E. (2025). dbplyr: A “dplyr” Back End for Databases [Computer software]. https://dbplyr.tidyverse.org/
readr v2.1.5 Wickham, H., Hester, J., & Bryan, J. (2025). readr: Read Rectangular Text Data [Computer software]. https://doi.org/10.32614/CRAN.package.readr
tidyr v1.3.1 Wickham, H., & Wickham, M. H. (2017). Package ‘tidyr.’ Easily Tidy Data with’spread’and’gather ()’Functions, 10.
stringr v1.5.2 Wickham, H., & Wickham, M. H. (2019). Package ‘stringr.’ Website: Http://Stringr. Tidyverse. Org, Https://Github. Com/Tidyverse/Stringr.
data.table v1.15.4 Wiley, M., & Wiley, J. F. (2020). Introduction to data. Table. In Advanced R 4 Data Programming and the Cloud: Using PostgreSQL, AWS, and Shiny (pp. 181–220). Springer.
rentrez v1.2.4 Winter, D. J. (2017). rentrez: An R package for the NCBI eUtils API. The R Journal, 9(2), 520–526. https://doi.org/10.32614/RJ-2017-058
