DspikeIn

This is the released version of DspikeIn; for the devel version, see DspikeIn.

Estimating Absolute Abundance from Microbial Spike-in Controls

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DOI: 10.18129/B9.bioc.DspikeIn

Bioconductor version: Release (3.22)

Provides a reproducible and modular workflow for absolute microbial quantification using spike-in controls. Supports both single spike-in taxa and synthetic microbial communities with user-defined spike-in volumes and genome copy numbers. Compatible with 'phyloseq' and 'TreeSummarizedExperiment' (TSE) data structures. The package implements methods for spike-in validation, preprocessing, scaling factor estimation, absolute abundance conversion, bias correction, and normalization. Facilitates downstream statistical analyses with 'DESeq2', 'edgeR', and other Bioconductor-compatible methods. Visualization tools are provided via 'ggplot2', 'ggtree', and related packages. Includes detailed vignettes, case studies, and function-level documentation to guide users through experimental design, quantification, and interpretation.

Author: Mitra Ghotbi [aut, cre] ORCID iD ORCID: 0000-0001-9185-9993 , Marjan Ghotbi [ctb] ORCID iD ORCID: 0000-0003-4655-6445

Maintainer: Mitra Ghotbi <mitra.ghotbi at gmail.com>

Citation (from within R, enter citation("DspikeIn")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("DspikeIn")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DspikeIn")

DspikeIn with TSE HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, DifferentialExpression, ExperimentalDesign, Microbiome, Normalization, Phylogenetics, Preprocessing, QualityControl, Sequencing, Software, Visualization

Version 1.0.0

In Bioconductor since BioC 3.22 (R-4.5) (< 6 months)

License MIT + file LICENSE

Depends R (>= 4.1.0)

Imports ape, Biostrings, data.table, DECIPHER, DESeq2, dplyr, edgeR, flextable, ggalluvial, ggnewscale, ggplot2, ggpubr, ggraph, ggrepel, ggridges, ggtree, ggtreeExtra, graphics, grDevices, igraph, limma, matrixStats, methods, microbiome, officer, grid, reshape2, patchwork, phangorn, phyloseq, randomForest, RColorBrewer, rlang, S4Vectors, scales, stats, tibble, tidyr, SummarizedExperiment, TreeSummarizedExperiment, utils, msa, xml2, ggstar

System Requirements

URL https://github.com/mghotbi/DspikeIn

Bug Reports https://github.com/mghotbi/DspikeIn/issues

Suggests Biobase, mia, BiocGenerics, magrittr, BiocManager, cluster, devtools, DT, e1071, foreach, ggtext, intergraph, knitr, optparse, plyr, preprocessCore, qpdf, remotes, rmarkdown, ShortRead, testthat (>= 3.0.0), vegan, viridis

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DspikeIn_1.0.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) DspikeIn_1.0.0.tgz

macOS Binary (arm64) DspikeIn_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/DspikeIn

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DspikeIn

Bioc Package Browser https://code.bioconductor.org/browse/DspikeIn/

Package Short Url https://bioconductor.org/packages/DspikeIn/

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Old Source Packages for BioC 3.22 Source Archive