DspikeIn
This is the development version of DspikeIn; for the stable release version, see DspikeIn.
Estimating Absolute Abundance from Microbial Spike-in Controls
Bioconductor version: Development (3.24)
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]
, Marjan Ghotbi [ctb]
Maintainer: Mitra Ghotbi <mitra.ghotbi at gmail.com>
citation("DspikeIn")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, DifferentialExpression, ExperimentalDesign, Microbiome, Normalization, Phylogenetics, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| 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 |
See More
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DspikeIn_1.3.0.tar.gz |
| Windows Binary (x86_64) | DspikeIn_1.3.0.zip |
| macOS Binary (big-sur-x86_64) | DspikeIn_1.3.0.tgz |
| macOS Binary (sonoma-arm64) | DspikeIn_1.3.0.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/ |
| Package Downloads Report | Download Stats |