Package: mire 0.0.1.9000

Yun Peng

mire: Microbiome Integrated Reconstruction and Estimation

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.

Authors:Yun Peng [aut, cre]

mire_0.0.1.9000.tar.gz
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mire_0.0.1.9000.tgz(r-4.6-x86_64)mire_0.0.1.9000.tgz(r-4.6-arm64)mire_0.0.1.9000.tgz(r-4.5-x86_64)mire_0.0.1.9000.tgz(r-4.5-arm64)
mire_0.0.1.9000.tar.gz(r-4.7-arm64)mire_0.0.1.9000.tar.gz(r-4.7-x86_64)mire_0.0.1.9000.tar.gz(r-4.6-arm64)mire_0.0.1.9000.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
card.svg |card.png
mire/json (API)
NEWS

# Install 'mire' in R:

install.packages('mire', repos = c('https://wanglabcsu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wanglabcsu/mire/issues

On CRAN:

rust cargo

3.30 score 4 stars 3 scripts 16 exports 65 dependencies

Last updated from:566070a04b. Checks:11 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	185
linux-devel-x86_64	WARNING	189
source / vignettes	OK	335
linux-release-arm64	WARNING	170
linux-release-x86_64	WARNING	180
macos-release-arm64	WARNING	186
macos-release-x86_64	WARNING	301
macos-oldrel-arm64	WARNING	101
macos-oldrel-x86_64	WARNING	352
windows-devel	WARNING	213
windows-release	WARNING	196
windows-oldrel	WARNING	223
wasm-release	FAIL	148

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