An integrated framework for microbiome reconstruction from sequencing data. It leverages tools like Kraken2 for taxonomic classification and combines cell barcodes, UMIs, and k-mer-based quantification to reconstruct microbial signals. Designed for both bulk and single-cell sequencing data, the package enables taxonomic and quantitative profiling of microbial communities.
Here, we use pak to install package, you can also use remotes:
if (!requireNamespace("pak")) {
install.packages("pak",
repos = sprintf(
"https://r-lib.github.io/p/pak/devel/%s/%s/%s",
.Platform$pkgType, R.Version()$os, R.Version()$arch
)
)
}You can install the development version from r-universe with:
pak::repo_add("https://wanglabcsu.r-universe.dev")
pak::pak("mire")or from GitHub with:
pak::pak("WangLabCSU/mire")You must also install kraken2.
sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-conda-linux-gnu
#> Running under: Ubuntu 26.04 LTS
#>
#> Matrix products: default
#> BLAS/LAPACK: /home/yun/.local/share/pixi/envs/r-release/lib/libopenblasp-r0.3.33.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.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_4.6.1 fastmap_1.2.0 cli_3.6.6 tools_4.6.1
#> [5] htmltools_0.5.9 otel_0.2.0 yaml_2.3.12 rmarkdown_2.31
#> [9] knitr_1.51 xfun_0.57 digest_0.6.39 rlang_1.3.0
#> [13] evaluate_1.0.5