Package: DspikeIn 1.3.1

Mitra Ghotbi

DspikeIn: Estimating Absolute Abundance from Microbial Spike-in Controls

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.

Authors:Mitra Ghotbi [aut, cre], Marjan Ghotbi [ctb]

DspikeIn_1.3.1.tar.gz
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DspikeIn_1.3.1.tgz(r-4.6-any)DspikeIn_1.3.1.tgz(r-4.5-any)
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DspikeIn_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DspikeIn/json (API)

# Install 'DspikeIn' in R:

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

Bug tracker:https://github.com/mghotbi/dspikein/issues

Datasets:

AcceptableRange - Acceptable Range Data
metadata_full - Metadata for Microbiome Samples
physeq - Example Phyloseq Object with Tree and Reference Sequences
physeq_16SOTU - Example Phyloseq Object for 16S OTUs
physeq_ITSOTU - Example Phyloseq Object for ITS OTUs
tse - Example TreeSummarizedExperiment (TSE) Object with Tree and Reference Sequences

On BioConductor:DspikeIn-1.3.0(bioc 3.24)DspikeIn-1.2.0(bioc 3.23)

microbiome preprocessing qualitycontrol differentialexpression normalization sequencing visualization phylogenetics experimentaldesign dataimport software absolute-abundances amplicon-sequencing gene-copies phylogenetic-trees qiime2 quantifying spike-ins transformation whole-cell

6.12 score 17 stars 26 scripts 61 exports 198 dependencies

Last updated from:b9e9e20ae4. Checks:1 NOTE, 7 ERROR, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	367
linux-devel-x86_64	ERROR	963
source / vignettes	OK	573
linux-release-x86_64	ERROR	896
macos-release-arm64	ERROR	596
macos-oldrel-arm64	ERROR	453
windows-devel	ERROR	957
windows-release	ERROR	890
windows-oldrel	ERROR	874
wasm-release	OK	213

Exports:adjust_abundance_by_factor adjust_abundance_one_third adjusted_prevalence alluvial_plot calculate_list_average_scaling_factors calculate_spike_percentage calculate_spike_percentage_list calculate_spikeIn_factors calculate_summary_stats_table color_palette conclusion convert_categorical_to_factors convert_phyloseq_to_tse convert_to_absolute_counts convert_tse_to_phyloseq create_directory degree_network detect_common_asvs_taxa extract_neighbors filter_and_split_abundance get_long_format_data get_otu_table get_phy_tree get_reference_seq get_sample_data get_sample_sums get_tax_table gm_mean imbalance_calculate_list_average_scaling_factors label load_graphml MG_shapes my_custom_theme node_level_metrics norm.DESeq normalization_set perform_and_visualize_DA plot_core_microbiome_custom plot_spikein_tree_diagnostic plotbar_abundance Pre_processing_hashcodes Pre_processing_species Pre_processing_species_list proportion_adj quadrant_plot random_subsample_WithReductionFactor RandomForest_selected randomsubsample_Trimmed_evenDepth regression_plot relativized_filtered_taxa remove_zero_negative_count_samples ridge_plot_it set_nf simulate_network_robustness summ_ASV_OTUID summ_count_phyloseq summ_phyloseq_sampleID taxa_barplot tidy_phyloseq_tse validate_spikein_clade weight_Network

Dependencies:abind ade4 ape aplot askpass backports base64enc bayesm BH Biobase BiocGenerics BiocParallel biomformat Biostrings boot broom bslib cachem car carData cli cluster codetools colorspace compositions corrplot cowplot cpp11 crayon data.table DBI DECIPHER DelayedArray DEoptimR Deriv DESeq2 digest doBy dplyr edgeR evaluate farver fastmap fastmatch flextable fontawesome fontBitstreamVera fontLiberation fontquiver foreach forecast formatR Formula fracdiff fs futile.logger futile.options gdtools generics GenomicRanges ggalluvial ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggridges ggsci ggsignif ggstar ggtree ggtreeExtra glue graphlayouts gridExtra gridGraphics gtable highr htmltools htmlwidgets igraph IRanges isoband iterators jquerylib jsonlite knitr labeling lambda.r lattice lazyeval lifecycle limma lme4 lmtest locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark microbiome mime minqa modelr msa MultipleAlignment multtest nlme nloptr nnet numDeriv officer openssl patchwork pbkrtest permute phangorn phyloseq pillar pixmap pkgconfig plyr polyclip polynom purrr quadprog quantreg R6 ragg randomForest rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas reshape2 rlang rmarkdown robustbase rstatix Rtsne S4Arrays S4Vectors S7 sass scales Seqinfo SingleCellExperiment snow sp SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys systemfonts tensorA textshaping tibble tidygraph tidyr tidyselect tidytree timeDate tinytex treeio TreeSummarizedExperiment tweenr urca utf8 uuid vctrs vegan viridis viridisLite withr xfun xml2 XVector yaml yulab.utils zip zoo

DspikeIn with TSE

Rendered fromDspikeIn-with-TSE.Rmdusingknitr::rmarkdown

Last update: 2026-06-23
Started: 2025-06-18

Help page	Topics
Acceptable Range Data	AcceptableRange
Adjust Abundance by a Custom Factor	adjust_abundance_by_factor adjust_abundance_one_third
Adjust Prevalence in a Microbiome Object	adjusted_prevalence
Generate an Alluvial Plot for Microbiome Data	alluvial_plot
Calculate Sample-specific Average Scaling Factors for Multiple Spike-in Groups	calculate_list_average_scaling_factors
Calculate Spike Percentage for Specified Taxa in a Phyloseq or TSE Object	calculate_spike_percentage
Calculate Spike-in Percentage for Specified Taxa	calculate_spike_percentage_list
Calculate Scaling Factors for Spiked Species in Phyloseq or TSE Object	calculate_spikeIn_factors
Calculate Summary Statistics Table	calculate_summary_stats_table
Original, Extended, and Nature-Inspired Color Palette Sequence	color_palette
Compute Summary Statistics for Spiked Species	conclusion
Convert Categorical Columns to Factors in Sample Data	convert_categorical_to_factors
Convert a 'phyloseq' Object to a 'TreeSummarizedExperiment'	convert_phyloseq_to_tse
Convert Relative ASV/OTU Counts to Absolute Counts	convert_to_absolute_counts
Convert a 'TreeSummarizedExperiment' to a 'phyloseq' Object	convert_tse_to_phyloseq
Create a Directory and Optionally Set as Working Directory	create_directory
Create a List from a Phyloseq or TSE Object	create_list
Analyze and Visualize a Microbial Network	degree_network
Detect Common ASVs and Taxa from Multiple Phyloseq or TSE Objects	detect_common_asvs_taxa
Extract First and Second Neighbors of a Target Node	extract_neighbors
Filter and Split Abundance Data by Threshold	filter_and_split_abundance
Convert a Phyloseq or TSE Object into a Long-Format Data Frame	get_long_format_data
Extract OTU Tax Metadata from Object	get_otu_table
Extract Phylogenetic Tree	get_phy_tree
Extract Reference Sequences	get_reference_seq
Extract Sample Data	get_sample_data
Extract Sample Sums from Object	get_sample_sums
Extract Taxonomy Table	get_tax_table
Calculate Geometric Mean	gm_mean
Calculate Per-Sample Scaling Factors for Multiple Spike-in Groups	imbalance_calculate_list_average_scaling_factors
Label Taxonomic Ranks by Hashcode	label
Load GraphML Without 'id' Conflicts	load_graphml
Metadata for Microbiome Samples	metadata_full
Predefined Shape Vector for Plot Styling	MG_shapes
Custom ggplot2 Theme with Consistent Aesthetics	my_custom_theme
Compute and Visualize Node-Level Network Metrics	node_level_metrics
CLR Normalization (Centered Log-Ratio Transformation)	norm.clr
CSS Normalization (Cumulative Sum Scaling)	norm.css
DESeq Normalization with Pseudocount and Integer Conversion	norm.DESeq
Median Normalization	norm.med
Poisson Normalization and Differential Abundance Function	norm.Poisson
Quantile Normalization (QN) for phyloseq object	norm.QN
Rarefying	norm.rar
RLE Normalization (Relative Log Expression)	norm.rle
TC Normalization (Total Count Scaling)	norm.TC
TMM Normalization (Trimmed Mean of M component)	norm.TMM
TSS Normalization (Total Sum Scaling)	norm.tss
UQ Normalization (Upper Quartile)	norm.UQ
Apply the Selected Normalization Method to the Phyloseq and TSE Objects	normalization_set
Perform and Visualize Differential Abundance Analysis with edgeR or DESeq2	perform_and_visualize_DA
Example Phyloseq Object with Tree and Reference Sequences	physeq
Example Phyloseq Object for 16S OTUs	physeq_16SOTU
Example Phyloseq Object for ITS OTUs	physeq_ITSOTU
Plot Core Microbiome Prevalence Heatmap (Phyloseq & TSE Compatible)	plot_core_microbiome_custom
Spike-in Tree Diagnostic Plot	plot_spikein_tree_diagnostic
Taxa Bar Plot Without Aggregation (Relative or Absolute Abundance)	plotbar_abundance
Pre-process phyloseq or TSE object based on hashcodes	Pre_processing_hashcodes
Pre-process taxa in a phyloseq or TSE object by merging ASVs/OTUs	Pre_processing_species
Preprocess and Merge Spike-in Species in a Phyloseq or TSE Object	Pre_processing_species_list
Proportionally Adjust Abundance	proportion_adj
Generate Custom Quadrant Plots for Node Metrics	quadrant_plot
Random Subsampling with Reduction Factor	random_subsample_WithReductionFactor
Select Important ASVs/OTUs Using Random Forest	RandomForest_selected
Subsampling to an Equal Sequencing Depth	randomsubsample_Trimmed_evenDepth
Create a Regression Plot with Faceting by Range	regression_plot
Filter Taxa from a Phyloseq or TSE Object Based on Custom Thresholds	relativized_filtered_taxa
Remove Samples with Zero, Negative Counts, or NA Values and Add Pseudocount	remove_zero_negative_count_samples
Generate Ridge Plots for Taxonomic Abundance Distribution	ridge_plot_it
Set Normalization Factors in the Sample Data of the Phyloseq Object	set_nf
Simulate Network Robustness under Node Removal	simulate_network_robustness
Summarize ASV Data Based on ASV_ID	summ_ASV_OTUID
Summary Statistics of a Phyloseq or TSE Object	summ_count_phyloseq
Generate Summary Statistics for Each Sample	summ_phyloseq_sampleID
Generate a Taxa Barplot with Relative or Absolute Abundance	taxa_barplot
Tidy a Phyloseq or TreeSummarizedExperiment Object	tidy_phyloseq_tse
Example TreeSummarizedExperiment (TSE) Object with Tree and Reference Sequences	tse
Validate Spike-In Clade Consistency with NJ Tree and Bootstrap	validate_spikein_clade
Analyze and Visualize a Microbial Network	weight_Network

Package: DspikeIn 1.3.1

DspikeIn: Estimating Absolute Abundance from Microbial Spike-in Controls

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