A computational resource designed to accurately detect microbial nucleic
acids while filtering out contaminants and false-positive taxonomic
assignments from standard transcriptomic sequencing of mammalian tissues
(See SAHMI). This implementation
leverages the polars package for fast and systematic microbial signal
recovery and denoising from host tissue genomic sequencing.
You can install rsahmi from CRAN using:
install.packages("rsahmi")Alternatively, install the development version from r-universe with:
install.packages("rsahmi",
repos = c("https://yunuuuu.r-universe.dev", "https://cloud.r-project.org")
)or from GitHub with:
# install.packages("remotes")
remotes::install_github("Yunuuuu/rsahmi")You must also install seqkit and kraken2.
Additionally, rsahmi relies on
polars. If you call any
functions that require polars, you will be prompted to install the
package.
If you use this package, please cite:
- Song, Yuxuan PhD; Peng, Yun PhD; Qin, Caipeng PhD; Jiang, Shan PhD; Lin, Jiaxing PhD; Lai, Shicong MD; Wu, Jilin PhD; Ding, Mengting PhD; Du, Yiqing PhD*; Yu, Luping MD*; Xu, Tao MD*. Antibiotic use attenuates response to immune checkpoint blockade in urothelial carcinoma via inhibiting CD74-MIF/COPA: revealing cross-talk between anti-bacterial immunity and ant-itumor immunity. International Journal of Surgery 111(1):p 972-987, January 2025. | DOI: 10.1097/JS9.0000000000001901.
- Ghaddar B, Blaser MJ, De S. Denoising sparse microbial signals from single-cell sequencing of mammalian host tissues. Nat Comput Sci. 2023 Sep;3(9):741-747. doi: 10.1038/s43588-023-00507-1. Epub 2023 Sep 18. PMID: 37946872; PMCID: PMC10634611.