DspikeIn
This is the development version of DspikeIn; to use it, please install the devel version of Bioconductor.
Estimating Absolute Abundance from Microbial Spike-in Controls
Bioconductor version: Development (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]
, Marjan Ghotbi [ctb]
Maintainer: Mitra Ghotbi <mitra.ghotbi at gmail.com>
citation("DspikeIn")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 0.99.29 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| 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_0.99.29.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | DspikeIn_0.99.29.tgz |
| macOS Binary (arm64) | DspikeIn_0.99.29.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 |