Package: rsahmi 0.0.2.9000

Yun Peng

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 rust 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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manual.pdf |manual.html✨
card.svg |card.png
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:

microbiome sahmi single-cell rust cargo

4.59 score 11 stars 79 downloads 17 exports 65 dependencies

Last updated from:a322ff5e16. Checks:11 ERROR, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	ERROR	141
linux-devel-x86_64	ERROR	140
source / vignettes	OK	225
linux-release-arm64	ERROR	147
linux-release-x86_64	ERROR	161
macos-release-arm64	ERROR	123
macos-release-x86_64	ERROR	318
macos-oldrel-arm64	ERROR	165
macos-oldrel-x86_64	ERROR	309
windows-devel	ERROR	171
windows-release	ERROR	320
windows-oldrel	ERROR	233
wasm-release	FAIL	119

Exports:blsd denoise_counts embed embed_trim koutreads kractor_koutput kractor_reads kraken2 krcount read_kreport rpmm_quantile seq_range seq_refine slsd tag taxa_counts trim

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops blit cigarillo cli codetools cpp11 crayon DelayedArray deldir farver formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable hwriter interp IRanges isoband jpeg labeling lambda.r lattice latticeExtra lifecycle MASS Matrix MatrixGenerics matrixStats mirai nanonext png processx ps pwalign R6 RColorBrewer Rcpp RcppEigen Rhtslib rlang Rsamtools S4Arrays S4Vectors S7 scales Seqinfo ShortRead snow SparseArray SummarizedExperiment vctrs viridisLite withr XVector

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Barcode level signal denoising	blsd
Denoise and Quantify Taxa from Kraken2 Results	denoise_counts
Kraken2 Output Processing for FASTQ Files	koutreads tag
Filter Kraken2 Output by Taxon	kractor_koutput
Extract Reads from Kraken2 Output Based on Classification	kractor_reads
Run Kraken2 for Taxonomic Classification	kraken2
Quantify K-mers and UMI Data by Taxon	krcount
Parse kraken report file	read_kreport
Identifying contaminants and false positives taxa (cell line quantile test)	rpmm_quantile
Create a UMI/Barcode range	seq_range
Refine Sequences from FASTQ Files with UMI/Barcode Actions	seq_refine
Sample level signal denoising	slsd
Define sequence range behavior: embed, trim, or both	embed embed_trim subseq_actions trim
Quantitation of microbes	taxa_counts