Single-cell Analysis of Host-Microbiome Interactions

⚠️ This package has been superseded by mire.
While rsahmi remains available for archival purposes, future development and improvements will be focused on mire, which offers an improved design for single-cell microbiome reconstruction and quantification.

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 rust for fast and systematic microbial signal recovery and denoising from host tissue genomic sequencing.

Installation

You can install rsahmi from CRAN using:

# install.packages("pak")
pak::pak("rsahmi")

Alternatively, install the development version from r-universe with:

pak::repo_add("https://yunuuuu.r-universe.dev")
pak::pak("rsahmi")

or from GitHub with:

pak::pak("Yunuuuu/rsahmi")

You must also install kraken2.

Cite

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.

sessionInfo

sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#> 
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so;  LAPACK version 3.8.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: Asia/Shanghai
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_4.4.2    fastmap_1.2.0     cli_3.6.5         tools_4.4.2      
#>  [5] htmltools_0.5.8.1 yaml_2.3.10       rmarkdown_2.29    knitr_1.50       
#>  [9] xfun_0.52         digest_0.6.37     rlang_1.1.6       evaluate_1.0.3