Package: rsahmi 0.0.2.9000

rsahmi: Single-Cell Analysis of Host-Microbiome Interactions

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. For more details, see Ghaddar (2023) <doi:10.1038/s43588-023-00507-1>. This implementation leverages the 'polars' package for fast and systematic microbial signal recovery and denoising from host tissue genomic sequencing.

Authors:Yun Peng [aut, cre]

rsahmi_0.0.2.9000.tar.gz

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rsahmi.pdf |rsahmi.html✨
rsahmi/json (API)
NEWS

# Install 'rsahmi' in R:
install.packages('rsahmi', repos = c('https://yunuuuu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yunuuuu/rsahmi/issues

On CRAN:

Conda:

microbiomesahmisingle-cell

3.90 score 13 downloads 10 exports 59 dependencies

Last updated 4 hours agofrom:85eeeae0e0. Checks:5 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 27 2025
R-4.5-macOKMar 27 2025
R-4.5-linuxOKMar 27 2025
R-4.4-macOKMar 27 2025
R-4.4-linuxOKMar 27 2025

Exports:blsdextract_kraken_outputextract_kraken_readsextract_taxidsparse_kraken_reportprep_datasetread_datasetremove_contaminantsslsdtaxa_counts

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsblitclicodetoolscpp11crayoncurldata.tableDelayedArraydeldirformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatsmimeopensslpngpwalignR6RColorBrewerRcppRcppEigenRhtslibrlangRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArraySummarizedExperimentsysUCSC.utilswithrXVector